[Cdd-commits] r450 - in projects/med/tags/0.13: . common debian debian/oldchangelogs debian/po.stub install menu menu/bio menu/bio-dev menu/cms menu/imaging menu/imaging-dev menu/physics menu/practice menu/tools tasks
CDD Subversion Commit
noreply at alioth.debian.org
Sat Aug 11 15:42:18 UTC 2007
Author: tille
Date: Sat Aug 11 15:42:18 2007
New Revision: 450
Added:
projects/med/tags/0.13/
projects/med/tags/0.13/AUTHORS
projects/med/tags/0.13/COPYING
projects/med/tags/0.13/VERSION
projects/med/tags/0.13/common/
projects/med/tags/0.13/common/common (contents, props changed)
projects/med/tags/0.13/common/common.1
projects/med/tags/0.13/common/conf
projects/med/tags/0.13/common/control
projects/med/tags/0.13/debian/
projects/med/tags/0.13/debian/changelog
projects/med/tags/0.13/debian/compat
projects/med/tags/0.13/debian/control (contents, props changed)
projects/med/tags/0.13/debian/control.stub
projects/med/tags/0.13/debian/copyright
projects/med/tags/0.13/debian/med-dent.config (contents, props changed)
projects/med/tags/0.13/debian/med-dent.install
projects/med/tags/0.13/debian/med-dent.manpages
projects/med/tags/0.13/debian/med-dent.postinst.stub
projects/med/tags/0.13/debian/med-dent.templates
projects/med/tags/0.13/debian/oldchangelogs/
projects/med/tags/0.13/debian/oldchangelogs/bio
projects/med/tags/0.13/debian/oldchangelogs/cms
projects/med/tags/0.13/debian/oldchangelogs/dent
projects/med/tags/0.13/debian/oldchangelogs/imaging
projects/med/tags/0.13/debian/oldchangelogs/imaging-dev
projects/med/tags/0.13/debian/oldchangelogs/tools
projects/med/tags/0.13/debian/po.stub/
projects/med/tags/0.13/debian/po.stub/POTFILES.in
projects/med/tags/0.13/debian/po.stub/de.po
projects/med/tags/0.13/debian/po.stub/templates.pot
projects/med/tags/0.13/debian/rules (contents, props changed)
projects/med/tags/0.13/install/
projects/med/tags/0.13/menu/
projects/med/tags/0.13/menu/bio/
projects/med/tags/0.13/menu/bio-dev/
projects/med/tags/0.13/menu/bio-dev/biomode.txt
projects/med/tags/0.13/menu/bio-dev/bioperl.txt
projects/med/tags/0.13/menu/bio-dev/libbio-ruby.txt
projects/med/tags/0.13/menu/bio-dev/libncbi6-dev.menu
projects/med/tags/0.13/menu/bio-dev/libvibrant6-dev.txt
projects/med/tags/0.13/menu/bio-dev/mcl.txt
projects/med/tags/0.13/menu/bio-dev/python-biopython.txt
projects/med/tags/0.13/menu/bio/blast2.menu
projects/med/tags/0.13/menu/bio/boxshade.txt
projects/med/tags/0.13/menu/bio/fastdnaml.html
projects/med/tags/0.13/menu/bio/fastlink.txt
projects/med/tags/0.13/menu/bio/gff2aplot.txt
projects/med/tags/0.13/menu/bio/gff2ps.txt
projects/med/tags/0.13/menu/bio/glimmer.txt
projects/med/tags/0.13/menu/bio/hmmer.txt
projects/med/tags/0.13/menu/bio/loki.txt
projects/med/tags/0.13/menu/bio/mipe.txt
projects/med/tags/0.13/menu/bio/molphy.txt
projects/med/tags/0.13/menu/bio/muscle.txt
projects/med/tags/0.13/menu/bio/ncbi-epcr.txt
projects/med/tags/0.13/menu/bio/ncbi-tools-bin.menu
projects/med/tags/0.13/menu/bio/ncbi-tools-x11.menu
projects/med/tags/0.13/menu/bio/phylip.txt
projects/med/tags/0.13/menu/bio/poa.txt
projects/med/tags/0.13/menu/bio/r-cran-qtl.txt
projects/med/tags/0.13/menu/bio/readseq.txt
projects/med/tags/0.13/menu/bio/sim4.txt
projects/med/tags/0.13/menu/bio/t-coffee.txt
projects/med/tags/0.13/menu/cms/
projects/med/tags/0.13/menu/cms/zope-zms.txt
projects/med/tags/0.13/menu/imaging/
projects/med/tags/0.13/menu/imaging-dev/
projects/med/tags/0.13/menu/imaging-dev/ctn-dev.txt
projects/med/tags/0.13/menu/imaging-dev/libgtkimreg-dev.txt
projects/med/tags/0.13/menu/imaging-dev/libmdc2-dev.txt
projects/med/tags/0.13/menu/imaging-dev/libminc0-dev.txt
projects/med/tags/0.13/menu/imaging/ctn.txt
projects/med/tags/0.13/menu/imaging/dcmtk.txt
projects/med/tags/0.13/menu/imaging/medcon.txt
projects/med/tags/0.13/menu/imaging/minc-tools.txt
projects/med/tags/0.13/menu/imaging/nifti-bin.txt
projects/med/tags/0.13/menu/physics/
projects/med/tags/0.13/menu/physics/octave.menu
projects/med/tags/0.13/menu/physics/r-base.menu
projects/med/tags/0.13/menu/practice/
projects/med/tags/0.13/menu/tools/
projects/med/tags/0.13/menu/tools/mencal.txt
projects/med/tags/0.13/tasks/
projects/med/tags/0.13/tasks/bio
projects/med/tags/0.13/tasks/bio-dev
projects/med/tags/0.13/tasks/cms
projects/med/tags/0.13/tasks/imaging
projects/med/tags/0.13/tasks/imaging-dev
projects/med/tags/0.13/tasks/pharmacy
projects/med/tags/0.13/tasks/physics
projects/med/tags/0.13/tasks/practice
projects/med/tags/0.13/tasks/tools
Log:
Tagged 0.13.
Added: projects/med/tags/0.13/AUTHORS
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/AUTHORS Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+Andreas Tille <tille at debian.org>
Added: projects/med/tags/0.13/COPYING
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/COPYING Sat Aug 11 15:42:18 2007
@@ -0,0 +1,340 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
Added: projects/med/tags/0.13/VERSION
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/VERSION Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+0.13
Added: projects/med/tags/0.13/common/common
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/common/common Sat Aug 11 15:42:18 2007
@@ -0,0 +1,6 @@
+#!/bin/sh
+## Prints some info about that package and lets auto-apt work
+dpkg --status `basename $0` | \
+ grep -v ^Priority | \
+ grep -v ^Section | \
+ grep -v ^Installed-Size
Added: projects/med/tags/0.13/common/common.1
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/common/common.1 Sat Aug 11 15:42:18 2007
@@ -0,0 +1,19 @@
+.TH med-common 1 "May 24, 2002" "Debian-Med"
+.SH NAME
+.B med-common
+.B med-<meta_package_name>
+\- package information and auto-apt helper
+
+.SH SYNOPSIS
+.B med-common
+.B med-<meta_package_name>
+
+.SH DESCRIPTION
+Print just a simple information page about every med-* package
+of the Debian-Med Custom Debian DIstribution. Each metapackage has a
+.I /usr/bin/med-<meta_package_name>
+file which should print some usefull informations and could be serve
+as auto-apt helper.
+
+.SH AUTHOR
+Andreas Tille <tille at debian.org>.
Added: projects/med/tags/0.13/common/conf
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/common/conf Sat Aug 11 15:42:18 2007
@@ -0,0 +1,9 @@
+## This is a configuration file for Debian-med Custom Debian Distribution
+## It is read after /etc/cdd/cdd.conf and can override or add variables
+
+## This variable is replaced by a debconf question
+## UPDATEUSERMENU=yes
+
+## Some CDDs do not build their name generic like Debian-#CDD# so
+## we need the correct name here
+CDDNAME=Debian-Med
Added: projects/med/tags/0.13/common/control
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/common/control Sat Aug 11 15:42:18 2007
@@ -0,0 +1,26 @@
+Package: med-common
+Architecture: all
+Depends: adduser, ${misc:Depends}, menu, cdd-common (>= 0.3.9)
+Description: Debian-Med Project common package
+ This package provides the basic infrastructure of all med-* packages and is
+ needed by them.
+ .
+ This package provides some files which are common to all med-* packages.
+ Moreover it introduces a method to handle system users in a group
+ med using debconf.
+ .
+ Other packages in Debian-Med Project are:
+ .
+ * med-bio for biological research
+ * med-cms for publicating a ... on the internet
+ * med-dent for dental medicine
+ * med-imaging for image processing
+ * med-pharmacy for pharmaceutical research
+ * med-physics for radiation oncology, diagnostics imaging and related fields
+ * med-practice for general practitioners
+ * med-tools contains miscellaneous tools
+ .
+ Note: All these packages are so called metapackages. This means they are not
+ executable programs, but only links to other packages. This way you will
+ conveniently get all the non-commercial medical software which is available
+ for Debian GNU/Linux.
Added: projects/med/tags/0.13/debian/changelog
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/changelog Sat Aug 11 15:42:18 2007
@@ -0,0 +1,163 @@
+debian-med (0.13) unstable; urgency=low
+
+ * Removed entry for gnumed-client-debug because this package does
+ not exist any more. Removed gnumed-client menu as well because
+ this should be builded automatically from menu entry inside
+ gnumed-client package
+ Closes: #429217
+ * Added several packages to med-bio and reordering the task to
+ specific fields
+ * Imaging: Added dicomnifti
+ * Enhanced long description of med-common
+ * Remove header from po.stub/de.po because cdd-dev will add another
+ one
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Jun 2007 16:23:36 +0200
+
+debian-med (0.12) unstable; urgency=low
+
+ * Changed med-practice menu
+ Closes: #385584
+ Use menu entry for gnumed-client-debug that regards #389932.
+ Note: gnumed-client-debug is not in the med-practice dependency
+ list but it is suggested by gnumed-client. So *if* the package
+ is installed at the box then an additional menu item occures correctly
+ in the Debian-Med menu. If it is not installed, only gnumed-client
+ is shown in the menu.
+ * med-bio: Added alternative to tree-puzzle as tree-ppuzzle
+ * Drop med-dent because odontolinux was removed from Debian
+ * med-bio: Added poa
+ Moved vrom Suggests to Depends: seaview (now really free)
+ Suggests: wise-doc
+ * med-imaging: Depends: libfslio0, libniftiio0, nifti-bin
+ Suggests:
+ * med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev
+ Suggests: libnifti-doc
+
+ -- Andreas Tille <tille at debian.org> Thu, 14 Sep 2006 15:28:51 +0200
+
+debian-med (0.11) unstable; urgency=low
+
+ * bugsx to from Depends to Suggets because this package moved to non-free
+ Closes: #383265
+ * Standards-Version: 3.7.2
+ Build-Depends: debhelper
+ * med-bio:
+ Depends: gromacs, dialign, kalign, probcons, wise, amap-align, biosquid
+ Suggests: mozilla-biofox
+ * debian/compat: 5
+ * Uploaders: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Aug 2006 10:07:41 +0200
+
+debian-med (0.10.1) unstable; urgency=low
+
+ * Make med-common depend from ${misc:Depends}
+ Closes: #331797
+ * Now med-practice really depends from gnumed-client which is now
+ awailable at Debian mirror
+
+ -- Andreas Tille <tille at debian.org> Wed, 5 Oct 2005 07:55:13 +0200
+
+debian-med (0.10) unstable; urgency=low
+
+ * Rebuilded with cdd-dev 0.3.11 (and increased versioned dependency
+ because 0.3.10 created broken *.dsc file)
+ Closes: #328428
+ * Standards-Version: 3.6.2 (no changes necessary)
+ * Added dependencies:
+ med-bio: mipe, sim4, perlprimer
+ med-bio-dev: libbio-ruby
+ * Addes meta package: med-practice
+
+ -- Andreas Tille <tille at debian.org> Sun, 25 Sep 2005 21:14:47 +0200
+
+debian-med (0.9) unstable; urgency=low
+
+ * Removed gnutrion from tools because it was removed from Debian at all
+ * Rebuilded with cdd-dev 0.3.10 version
+ * med-bio:
+ Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
+ Suggests: arb
+ * med-bio-dev
+ Recommends: libvibrant6-dev
+ Why: libmotif-dev conflicts lesstif-dev, so if someone wants to
+ install libmotif-dev it must be possible to deinstall
+ libvibrant6-dev without beeing forced to deinstall med-bio-dev
+ as well
+ Depends: python-biopython
+ * med-imaging:
+ paul now Recommends not Depends
+ Depends: dcmtk
+ Recommends: pngquant
+ * med-tools:
+ Depends: cycle
+ Suggests: cl-pubmed
+ Strong dependency would cost installing a large amount
+ of Common Lisp tools which in most cases is not worth
+ the effort
+ * Added user menu entries: bio/gff2aplot.txt, bio/gff2ps.txt,
+ bio/muscle.txt, bio/t-coffee.txt, bio/boxshade.txt,
+ bio-dev/python-biopython.txt, imaging/dcmtk.txt
+ * Added charset to debian/po.stub/de.po
+
+ -- Andreas Tille <tille at debian.org> Sun, 24 Oct 2004 20:59:03 +0200
+
+debian-med (0.8.9) experimental; urgency=low
+
+ * New upstream version which now uses the features of cdd-dev 0.3.9
+ * Exclude .svn dirs in dist target of debian/rules
+
+ -- Andreas Tille <tille at debian.org> Fri, 16 Jul 2004 11:33:21 +0200
+
+debian-med (0.8.3) unstable; urgency=high
+
+ * Rebuilded again against cdd-dev 0.3.4 which really closes the
+ mentioned bug.
+ * Urgency set to high because it *really* fixes a grave bug.
+
+ -- Andreas Tille <tille at debian.org> Thu, 15 Jul 2004 10:59:25 +0200
+
+debian-med (0.8.2) unstable; urgency=high
+
+ * Rebuilded with cdd-dev 0.3.3 which closes a grave bug (which
+ was reassigned to cdd-dev and thus it is not closed in this
+ changelog).
+ * Please make sure that all ${HOME}/.menu/cdd-menu files or
+ ${HOME}/.menu/med-* files are removed - they will not be
+ needed any more.
+
+ -- Andreas Tille <tille at debian.org> Wed, 14 Jul 2004 21:42:24 +0200
+
+debian-med (0.8.1) unstable; urgency=low
+
+ * Adjust versioned dependency of med-common from cdd-common
+ Closes: #258373
+
+ -- Andreas Tille <tille at debian.org> Fri, 9 Jul 2004 09:18:49 +0200
+
+debian-med (0.8) unstable; urgency=low
+
+ * Added med-physics, med-pharmacy, med-bio-dev
+ * Overworked menus of meta packages
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Jun 2004 14:44:36 +0200
+
+debian-med (0.7) unstable; urgency=low
+
+ * Switched to new version of cdd package (0.3) which has many
+ enhancements (no really important changes to the Debian-Med stuff
+ except that the packages have to be rebuilded with cdd-dev).
+ * New cdd-dev package cares for versioned dependency on med-common
+ Closes: #244903
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Apr 2004 11:21:16 +0200
+
+debian-med (0.6) unstable; urgency=medium
+
+ * Took over Debian-Edu method to build metapackages from one
+ common source.
+ The changelogs of the previous single meta package sources
+ can be found in the source package under debian/oldchangelogs.
+
+ -- Andreas Tille <tille at debian.org> Mon, 22 Mar 2004 19:21:55 +0100
Added: projects/med/tags/0.13/debian/compat
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/compat Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+5
Added: projects/med/tags/0.13/debian/control
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/control Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+link control.stub
\ No newline at end of file
Added: projects/med/tags/0.13/debian/control.stub
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/control.stub Sat Aug 11 15:42:18 2007
@@ -0,0 +1,11 @@
+Source: debian-med
+Section: misc
+Priority: extra
+Maintainer: Andreas Tille <tille at debian.org>
+Uploaders: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Build-Depends: debhelper (>= 5)
+Build-Depends-Indep: cdd-dev (>= 0.3.11)
+Standards-Version: 3.7.2
+
+Package: med
+Architecture: all
Added: projects/med/tags/0.13/debian/copyright
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/copyright Sat Aug 11 15:42:18 2007
@@ -0,0 +1,5 @@
+This package is Copyright 2004 by Andreas Tille <tille at debian.org>
+
+This software is licensed under the GPL.
+
+On Debian systems, the GPL can be found at /usr/share/common-licenses/GPL.
Added: projects/med/tags/0.13/debian/med-dent.config
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/med-dent.config Sat Aug 11 15:42:18 2007
@@ -0,0 +1,20 @@
+#!/bin/sh
+set -e
+
+CFGDIR=/etc/cdd/med/tasks/dent/
+CFG=${CFGDIR}/odontolinux.conf
+PKG=`basename $0 | sed -e 's/\.[^.]*$//'`
+
+DEBCONF_DEBUG=developer
+
+. /usr/share/debconf/confmodule
+db_version 2.0
+
+if [ -e ${CFG} ]; then
+ . ${CFG} || true
+ if [ "$SERVER" ] ; then
+ db_set ${PKG}/server $SERVER
+ fi
+fi
+db_input medium ${PKG}/server || true
+db_go || true
Added: projects/med/tags/0.13/debian/med-dent.install
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/med-dent.install Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+install/dent/dentalpractice usr/bin
Added: projects/med/tags/0.13/debian/med-dent.manpages
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/med-dent.manpages Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+install/dent/dentalpractice.1
Added: projects/med/tags/0.13/debian/med-dent.postinst.stub
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/med-dent.postinst.stub Sat Aug 11 15:42:18 2007
@@ -0,0 +1,32 @@
+#!/bin/sh
+set -e
+
+CFGDIR=/etc/cdd/med/tasks/dent/
+CFG=${CFGDIR}/odontolinux.conf
+PKG=`basename $0 | sed -e 's/\.[^.]*$//'`
+
+DEBCONF_DEBUG=developer
+. /usr/share/debconf/confmodule
+db_version 2.0
+
+NEW=0
+if [ -e "${CONF}" ]; then
+ NEW=-1
+ . ${CFG} || true
+fi
+
+# Handle server variable in config file
+db_get ${PKG}/server
+if [ ${NEW} ] ; then
+ mkdir -p ${CFGDIR}
+ cat > ${CFG} <<EOT
+# Configuration for Odontolinux
+# SERVER is the host which is running the Odontolinux system.
+# The default host is localhost.
+SERVER=$RET
+EOT
+fi
+
+db_go
+
+#DEBHELPER#
Added: projects/med/tags/0.13/debian/med-dent.templates
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/med-dent.templates Sat Aug 11 15:42:18 2007
@@ -0,0 +1,8 @@
+Template: med-dent/server
+Type: string
+Default: localhost
+_Description: Host running the Odontolinux! server:
+ Odontolinux is a dental office management software which runs on a
+ server and will be accessed by a web browser. Please input the
+ host name on which the Odontolinux server is running. If Odontolinux
+ is running on this host you can go with the defaul (localhost).
Added: projects/med/tags/0.13/debian/oldchangelogs/bio
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/bio Sat Aug 11 15:42:18 2007
@@ -0,0 +1,95 @@
+med-bio (0.5-6) unstable; urgency=low
+
+ * Added depends: ncbi-epcr, r-cran-qtl
+
+ -- Andreas Tille <tille at debian.org> Fri, 13 Feb 2004 12:11:37 +0100
+
+med-bio (0.5-5) unstable; urgency=low
+
+ * Added:
+ Depends: loki, tigr-glimmer
+ Suggests: r-base-core
+
+ -- Andreas Tille <tille at debian.org> Wed, 14 Jan 2004 08:31:37 +0100
+
+med-bio (0.5-4) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Depend from further packages:
+ blast2, ncbi-tools-bin, ncbi-tools-x11
+ * Standards-Version: 3.5.9
+ * debian/compat now stores debhelper compatibility version
+
+ -- Andreas Tille <tille at debian.org> Fri, 4 Apr 2003 08:21:01 +0200
+
+med-bio (0.5-2) unstable; urgency=low
+
+ * Depend from further packages:
+ bioperl, hmmer, rasmol
+ * Standards-Version: 3.5.8
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Jan 2003 21:37:07 +0100
+
+med-bio (0.5-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Mon, 24 Jun 2002 17:00:19 +0200
+
+med-bio (0.4-3) unstable; urgency=low
+
+ * Added list of dependend packages to package description.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 21:53:41 +0200
+
+med-bio (0.4-2) unstable; urgency=low
+
+ * Added pymol to dependencies.
+ * Introduces /usr/bin/med-bio
+ to give auto-apt a chance to install the package
+ * Manpage for this script.
+ * Remark regarding to the menu entry which was introduced in the last
+ version:
+ The policy violation will be removed and we (Ben Amstrong - Debian-Jr
+ initiator and me) decided to find a better, i.e. user based, menu
+ system.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 20:45:57 +0200
+
+med-bio (0.4-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 12:24:01 +0200
+
+med-bio (0.3-1) unstable; urgency=low
+
+ * Added garlic
+
+ -- Andreas Tille <tille at debian.org> Fri, 19 Apr 2002 15:06:27 +0200
+
+med-bio (0.2-1) unstable; urgency=low
+
+ * Added bugsx
+
+ -- Andreas Tille <tille at debian.org> Sun, 14 Apr 2002 18:44:55 +0200
+
+med-bio (0.1-2) unstable; urgency=low
+
+ * Added biomode, fastdnaml
+
+ -- Andreas Tille <tille at debian.org> Fri, 8 Feb 2002 08:29:38 +0100
+
+med-bio (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132669
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/0.13/debian/oldchangelogs/cms
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/cms Sat Aug 11 15:42:18 2007
@@ -0,0 +1,6 @@
+med-cms (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #226464
+
+ -- Andreas Tille <tille at debian.org> Tue, 6 Jan 2004 11:03:42 +0100
Added: projects/med/tags/0.13/debian/oldchangelogs/dent
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/dent Sat Aug 11 15:42:18 2007
@@ -0,0 +1,60 @@
+med-dent (0.5-2) unstable; urgency=low
+
+ * Added French debconf translation
+ Closes: #236301
+ * Reenabled user menu via med_install_helper
+
+ -- Andreas Tille <tille at debian.org> Tue, 9 Mar 2004 09:17:33 +0100
+
+med-dent (0.5-1) unstable; urgency=low
+
+ * Switched to new debconf format (Thanks to
+ Martin Quinson <Martin.Quinson at tuxfamily.org>
+ for the patch.
+ Closes: Ã#234757
+ * Standards-Version: 3.6.1
+ * Depends: debianutils, mozilla-browser | www-browser
+ instead of galeon | www-browser
+ * med-dent script now uses sensible-browser
+ * used debian/install, debian/manpages, debian/compat
+
+ -- Andreas Tille <tille at debian.org> Thu, 26 Feb 2004 08:23:56 +0100
+
+med-dent (0.4-1) unstable; urgency=low
+
+ * Do not depend from Odontolinux! but ask user for the server name which
+ hosts the Odontolinux! server
+ Closes: #167585
+
+ -- Andreas Tille <tille at debian.org> Wed, 25 Dec 2002 11:07:15 +0100
+
+med-dent (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 17:38:44 +0200
+
+med-dent (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Dent menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+ * Depends www-browser
+
+ -- Andreas Tille <tille at debian.org> Sat, 18 May 2002 17:53:56 +0200
+
+med-dent (0.1-2) unstable; urgency=low
+
+ * move to section misc instead of doc (where it stupidly landed)
+
+ -- Andreas Tille <tille at debian.org> Fri, 22 Feb 2002 12:14:35 +0100
+
+med-dent (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #132667
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/0.13/debian/oldchangelogs/imaging
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/imaging Sat Aug 11 15:42:18 2007
@@ -0,0 +1,70 @@
+med-imaging (0.4-4) unstable; urgency=low
+
+ * Removed rumbaview which was removed from Debian
+ closes: #214229
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Oct 2003 20:38:28 +0200
+
+med-imaging (0.4-3) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added minc-tools, medcon, xmedcon
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 10:54:27 +0200
+
+med-imaging (0.4-2) unstable; urgency=low
+
+ * Really *Depends* from med-common, which was just a typo to add
+ it to Suggests - list
+ closes: #151881
+ * Fixes typo in description
+ closes: #152614
+
+ -- Andreas Tille <tille at debian.org> Wed, 24 Jul 2002 13:54:32 +0200
+
+med-imaging (0.4-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+ * Forgot to mention newly added ctsim package in package description.
+ * Added ctn to dependencies.
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jun 2002 16:21:14 +0200
+
+med-imaging (0.3-1) unstable; urgency=low
+
+ * Added ctsim to dependencies
+ * Introduces /usr/bin/med-imaging
+ to give auto-apt a chance to install the package
+ * Manpage for this script.
+ * Remark regarding to the menu entry which was introduced in the last
+ version:
+ The policy violation will be removed and we (Ben Amstrong - Debian-Jr
+ initiator and me) decided to find a better, i.e. user based, menu
+ system.
+
+ -- Andreas Tille <tille at debian.org> Tue, 28 May 2002 07:23:05 +0200
+
+med-imaging (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+ * Added some information about rumbaview which is quite sparse in the
+ package itself.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 09:34:32 +0200
+
+med-imaging (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142458
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
Added: projects/med/tags/0.13/debian/oldchangelogs/imaging-dev
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/imaging-dev Sat Aug 11 15:42:18 2007
@@ -0,0 +1,58 @@
+med-imaging-dev (0.3-4) unstable; urgency=low
+
+ * Removed librumba-dev from dependencies because it was removed from Debian
+ closes: #214230
+
+ -- Andreas Tille <tille at debian.org> Sun, 5 Oct 2003 20:45:59 +0200
+
+med-imaging-dev (0.3-3) unstable; urgency=low
+
+ * What difference does it make to the dead, the orphans and the homeless,
+ whether the mad destruction is wrought under the name of totalitarianism
+ or the holy name of liberty or democracy?
+ -- Mahatma Gandhi (1869 - 1948), "Non-Violence in Peace and War"
+ * Changed dependency from libmdc-dev to libmdc2-dev
+ closes: #190240
+
+ -- Andreas Tille <tille at debian.org> Wed, 23 Apr 2003 13:25:30 +0200
+
+med-imaging-dev (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added libmdc-dev, libminc0-dev
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 11:12:52 +0200
+
+med-imaging-dev (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+ * Added ctn-dev to to dependencies.
+ * "avoids" #150864
+ It does not close the bug because it is an enlightenment bug and so
+ it will be reassigned. But the bug will not show up any more with this
+ package because the menu section was renamed.
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jun 2002 16:18:18 +0200
+
+med-imaging-dev (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:43:59 +0200
+
+med-imaging-dev (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142459
+
+ -- Andreas Tille <tille at debian.org> Thu, 11 Apr 2002 17:45:50 +0200
Added: projects/med/tags/0.13/debian/oldchangelogs/tools
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/oldchangelogs/tools Sat Aug 11 15:42:18 2007
@@ -0,0 +1,42 @@
+med-tools (0.3-3) unstable; urgency=low
+
+ * Removed dependency on gnutrion
+ closes: #199107
+
+ -- Andreas Tille <tille at debian.org> Sun, 29 Jun 2003 07:45:53 +0200
+
+med-tools (0.3-2) unstable; urgency=low
+
+ * The "I'm against war" release
+ Mankind must put an end to war before war puts an end to mankind.
+ -- John F. Kennedy
+ * Standards-Version: 3.5.9
+ * Added gnutrition
+ * debian/compat now stores debhelper compatibility version
+ * Build-Depends: debhelper (>= 4)
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2003 09:40:43 +0200
+
+med-tools (0.3-1) unstable; urgency=low
+
+ * First attempt to use user menus unsing med-common package.
+ * Build-Depends-Indep med-common-dev to make building stuff more general
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jun 2002 23:21:16 +0200
+
+med-tools (0.2-1) unstable; urgency=low
+
+ * Introduced Med/Microbiology menu
+ In the current form it forces a lintian error because it introduces
+ a new root menu section. I just want to show this as a suggestion in
+ some talks and afterwards will follow the consensus which might be
+ result in a policy change.
+
+ -- Andreas Tille <tille at debian.org> Sun, 19 May 2002 21:45:18 +0200
+
+med-tools (0.1-1) unstable; urgency=low
+
+ * Initial release
+ closes: #142901
+
+ -- Andreas Tille <tille at debian.org> Wed, 6 Feb 2002 20:56:59 +0100
Added: projects/med/tags/0.13/debian/po.stub/POTFILES.in
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/po.stub/POTFILES.in Sat Aug 11 15:42:18 2007
@@ -0,0 +1 @@
+[type: gettext/rfc822deb] med-dent.templates
Added: projects/med/tags/0.13/debian/po.stub/de.po
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/po.stub/de.po Sat Aug 11 15:42:18 2007
@@ -0,0 +1,34 @@
+#
+# Translators, if you are not familiar with the PO format, gettext
+# documentation is worth reading, especially sections dedicated to
+# this format, e.g. by running:
+# info -n '(gettext)PO Files'
+# info -n '(gettext)Header Entry'
+#
+# Some information specific to po-debconf are available at
+# /usr/share/doc/po-debconf/README-trans
+# or http://www.debian.org/intl/l10n/po-debconf/README-trans
+#
+# Developers do not need to manually edit POT or PO files.
+#
+
+#. Type: string
+#. Description
+#: ../med-dent.templates:1001
+msgid "Host running the Odontolinux! server:"
+msgstr "Rechner auf dem der Odontolinux! server läuft:"
+
+#. Type: string
+#. Description
+#: ../med-dent.templates:1001
+msgid ""
+"Odontolinux is a dental office management software which runs on a server "
+"and will be accessed by a web browser. Please input the host name on which "
+"the Odontolinux server is running. If Odontolinux is running on this host "
+"you can go with the defaul (localhost)."
+msgstr ""
+"Odontolinux ist ein Verwaltungssystem für die zahnärztliche Praxis, das auf "
+"einem Server läuft und über einen Web-Browser bedient wird. Bitte geben Sie "
+"den Rechnernamen ein, auf dem der Odontolinux server läuft. Falls "
+"Odontolinux auf diesem Server läuft, kann der Standardwert (localhost) "
+"beibehalten werden."
Added: projects/med/tags/0.13/debian/po.stub/templates.pot
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/po.stub/templates.pot Sat Aug 11 15:42:18 2007
@@ -0,0 +1,33 @@
+# SOME DESCRIPTIVE TITLE.
+# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL at ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"Report-Msgid-Bugs-To: tille at debian.org\n"
+"POT-Creation-Date: 2006-08-16 10:47+0200\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL at ADDRESS>\n"
+"Language-Team: LANGUAGE <LL at li.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=CHARSET\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: string
+#. Description
+#: ../med-dent.templates:1001
+msgid "Host running the Odontolinux! server:"
+msgstr ""
+
+#. Type: string
+#. Description
+#: ../med-dent.templates:1001
+msgid ""
+"Odontolinux is a dental office management software which runs on a server "
+"and will be accessed by a web browser. Please input the host name on which "
+"the Odontolinux server is running. If Odontolinux is running on this host "
+"you can go with the defaul (localhost)."
+msgstr ""
Added: projects/med/tags/0.13/debian/rules
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/debian/rules Sat Aug 11 15:42:18 2007
@@ -0,0 +1,79 @@
+#!/usr/bin/make -f
+# debian/rules for Debian-Med.
+# GNU copyright 2004 Andreas Tille, GPL.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+cdd=med
+pkgsrc=debian-$(cdd)
+
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+
+ cdd-gen-control -c -m -i -t
+
+ touch build-stamp
+
+clean: debian/control tasks/* debian/control.stub
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ cdd-clean-helper
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+# Build architecture-dependent files here.
+binary-arch: build install
+# We have nothing to do by default.
+
+# Build architecture-independent files here.
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+ dh_installdocs
+ dh_installexamples
+ dh_installmenu
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_installinit
+ dh_installcron
+ dh_installman
+ cdd-install-helper
+ dh_install
+ dh_installdebconf
+# dh_installinfo
+ dh_installchangelogs
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_makeshlibs
+ dh_installdeb
+# dh_perl
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+dist:
+ distdir=$(pkgsrc)-`cat VERSION` ; \
+ rm -rf $${distdir} ; \
+ mkdir $${distdir} ; \
+ chmod 777 $${distdir} ; \
+ rsync -a --exclude $${distdir} --exclude CVS --exclude .svn * $${distdir} ; \
+ ln -s control.stub $${distdir}/debian/control ; \
+ GZIP=-9 tar -czf ../$(pkgsrc)_`cat VERSION`.tar.gz $${distdir} ; \
+ rm -rf $${distdir}
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Added: projects/med/tags/0.13/menu/bio-dev/biomode.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/biomode.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,11 @@
+BioMode: Emacs mode to edit genetic data
+
+Some information about Biomode from the Debian-Med project.
+
+ It provides you several interesting commands to take the antiparallel
+ of a region, convert it using readseq, runs blast on it, etc.
+
+This package is not really installed by the med-bio package but it is
+suggested. That means if you are comfortable with the powerful editor
+Emacs you might wish to install also the biomode package and make use
+of it by typing "M-x biomode".
Added: projects/med/tags/0.13/menu/bio-dev/bioperl.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/bioperl.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,13 @@
+Bioperl: Perl tools for computational molecular biology
+
+Some information about Bioperl from the Debian-Med project.
+
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules.
+
+The Homepage is http://bio.perl.org/
+
+You can get a good overview by the main manpage:
+
+ man bioperl
Added: projects/med/tags/0.13/menu/bio-dev/libbio-ruby.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/libbio-ruby.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+BioRuby tools for computational molecular biology
+
+Some information about libbio-ruby from the Debian-Med project.
+
+ BioRuby project aims to implement an integrated environment for
+ Bioinformatics with Ruby language. Design philosophy of the BioRuby library
+ is KISS (keep it simple and stupid) to maximize the usability and the
+ efficiency for biologists as a daily tool. The project was started in Japan
+ and supported by University of Tokyo (Human Genome Center), Kyoto University
+ (Bioinformatics Center) and the Open Bio Foundation.
+
+Homepage: http://www.bioruby.org/
Added: projects/med/tags/0.13/menu/bio-dev/libncbi6-dev.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/libncbi6-dev.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,4 @@
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/asntool" needs="X11" \
+ section="Med/Biology development" title="asntool" hints="Biology" icon="/usr/share/pixmaps/asntool.xpm"
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/errhdr" needs="X11" \
+ section="Med/Biology development" title="errhdr" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/0.13/menu/bio-dev/libvibrant6-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/libvibrant6-dev.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,13 @@
+libvibrant6-dev: NCBI libraries for graphic biology applications
+ (development files)
+
+Some information about libvibrant6-dev from the Debian-Med project.
+
+ Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
+ biological applications.
+
+The Homepage is http://www.ncbi.nlm.nih.gov/
+
+You can get a good overview by reading
+
+ zless /usr/share/doc/libvibrant6-dev/README.gz
Added: projects/med/tags/0.13/menu/bio-dev/mcl.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/mcl.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,33 @@
+MCL: Markov Cluster algorithm
+
+Some information about mcl from the Debian-Med project.
+
+ The MCL package is an implementation of the MCL algorithm, and offers
+ utilities for manipulating sparse matrices (the essential data
+ structure in the MCL algorithm) and conducting cluster experiments.
+
+ MCL is currently being used in sciences like biology (protein family
+ detection, genomics), computer sciense (node clustering in
+ Peer-to-Peer networks), and linguistics (text analysis).
+
+ Homepage: http://micans.org/mcl/
+
+An overview about the various tools are given by the following manpages:
+
+ man mcx
+ man clmimac
+ man clmmate
+ man clmmeet
+ man clmformat
+ man clmdist
+ man clminfo
+ man mcxconvert
+ man mcxassemble
+ man mcxmap
+ man mcxsubs
+ man mcxarray
+ man mcxdeblast
+ man mclblastline
+ man mcl
+ man clmresidue
+ man mclpipeline
Added: projects/med/tags/0.13/menu/bio-dev/python-biopython.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio-dev/python-biopython.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,18 @@
+Python library for bioinformatics
+
+Some information about python-biopython from the Debian-Med project.
+
+ The Biopython Project is an international association
+ of developers of freely available Python tools for
+ computational molecular biology.
+
+ It is a distributed collaborative effort to develop Python
+ libraries and applications which address the needs of
+ current and future work in bioinformatics. The source code
+ is made available under the Biopython License, which is
+ extremely liberal and compatible with almost every license
+ in the world. We work along with the Open Bioinformatics
+ Foundation, who generously provide web and CVS space for
+ the project.
+
+Homepage: http://biopython.org/
Added: projects/med/tags/0.13/menu/bio/blast2.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/blast2.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,29 @@
+# The lot of entries just blast the menu to much
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/bl2seq" needs="X11" \
+ section="Med/Biology/Blast2" title="bl2seq" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blast2" needs="X11" \
+ section="Med/Biology/Blast2" title="blast2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastall" needs="X11" \
+ section="Med/Biology/Blast2" title="blastall" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastcl3" needs="X11" \
+ section="Med/Biology/Blast2" title="blastcl3" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastclust" needs="X11" \
+ section="Med/Biology/Blast2" title="blastclust" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastpgp" needs="X11" \
+ section="Med/Biology/Blast2" title="blastpgp" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/copymat" needs="X11" \
+ section="Med/Biology/Blast2" title="copymat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastacmd" needs="X11" \
+ section="Med/Biology/Blast2" title="fastacmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/formatdb" needs="X11" \
+ section="Med/Biology/Blast2" title="formatdb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/impala" needs="X11" \
+ section="Med/Biology/Blast2" title="impala" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makemat" needs="X11" \
+ section="Med/Biology/Blast2" title="makemat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/megablast" needs="X11" \
+ section="Med/Biology/Blast2" title="megablast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/rpsblast" needs="X11" \
+ section="Med/Biology/Blast2" title="rpsblast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/seedtop" needs="X11" \
+ section="Med/Biology/Blast2" title="seedtop" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/0.13/menu/bio/boxshade.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/boxshade.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+Pretty-printing of multiple sequence alignments
+
+Some information about boxshade from the Debian-Med project.
+
+ Boxshade reads a sequence alignment as input (e.g. from ClustalW) and
+ outputs files that may be incorporated to text processing software
+ (TeX via xfig, Word and OpenOffice via RTF). The post script format
+ is also supported.
+
+See also: man boxshade
+
+Homepage: http://www.ch.embnet.org/software/BOX_form.html
Added: projects/med/tags/0.13/menu/bio/fastdnaml.html
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/fastdnaml.html Sat Aug 11 15:42:18 2007
@@ -0,0 +1,44 @@
+<html>
+<head>
+<title>Construction of Phylogenetic Trees</title>
+<meta name="author" content="Andreas Tille" />
+</head>
+<body>
+<h2>FastDNAml: Construction of Phylogenetic Trees</h2>
+
+<h3>Some information about fastDNAml from the Debian-Med project.</h3>
+
+<h4>fastdnaml provides tools for construction of phylogenetic trees of DNA sequences</h4>
+
+<quote>
+ fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+ (part of his PHYLIP package). Users should consult the documentation for
+ DNAML before using this program.
+ fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+ faster and using less memory, so that larger trees and/or more bootstrap
+ replicates become tractable. Much of fastDNAml is merely a recoding of the
+ PHYLIP 3.3 DNAML program from PASCAL to C.
+</quote>
+
+<h4>For more detailed information see</h4>
+
+<example>
+ man fastDNAml
+ man fastDNAml-util
+ view /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt.gz
+</example>
+
+ or test the examples under
+
+<example>
+ /usr/share/doc/fastdnaml/examples
+</example>
+
+ using the Makefile provided under
+
+<example>
+ /usr/share/doc/fastdnaml/examples/tests
+</example>
+</body>
+</html>
+
Added: projects/med/tags/0.13/menu/bio/fastlink.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/fastlink.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,14 @@
+FastLink: Faster Pedigree
+
+Some information about fastlink from the Debian-Med project.
+
+ A faster version of pedigree programs of Linkage
+ Fastlink is much faster than the original Linkage but does not
+ implement all the programs.
+
+Unfortunately there is no manpage for the included tools which are
+ ilink, linkmap, lodscore, mlink
+
+Extensive documentation inclusive PostScript formatted papers are provided under
+
+ /usr/share/doc/fastlink
Added: projects/med/tags/0.13/menu/bio/gff2aplot.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/gff2aplot.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,11 @@
+Pair-wise alignment-plots for genomic sequences in PostScript
+
+Some information about gff2aplot from the Debian-Med project.
+
+ A program to visualize the alignment of two genomic sequences together with
+ their annotations. From GFF-format input files it produces PostScript figures
+ for that alignment.
+
+See also: man gff2aplot
+
+Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Added: projects/med/tags/0.13/menu/bio/gff2ps.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/gff2ps.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,16 @@
+Produce PostScript graphical output from GFF-files
+
+Some information about gff2ps from the Debian-Med project.
+
+ gff2ps is a script program developed with the aim of converting gff-formatted
+ records into high quality one-dimensional plots in PostScript. Such plots
+ maybe useful for comparing genomic structures and to visualizing outputs from
+ genome annotation programs.
+ It can be used in a very simple way, because it assumes that the GFF file
+ itself carries enough formatting information, but it also allows through a
+ number of options and/or a configuration file, for a great degree of
+ customization.
+
+See also: man gff2ps
+
+Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html
Added: projects/med/tags/0.13/menu/bio/glimmer.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/glimmer.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,32 @@
+Tigr Glimmer: Gene detection in archea and bacteria
+
+Some information about tigr-glimmer from the Debian-Med project.
+
+ Developed by the TIGR institute this software detects coding sequences in
+ bacteria and archea.
+
+ Glimmer is a system for finding genes in microbial DNA, especially the
+ genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated
+ Markov Modeler) uses interpolated Markov models (IMMs) to identify the
+ coding regions and distinguish them from noncoding DNA.
+
+ Homepage: http://www.tigr.org/software/glimmer/
+
+An overview about the various tools are given by the following manpages:
+
+ man glimmer2 (start with this)
+ man build-icm
+ man extract
+ man long-orfs
+
+More or less simple syntax help without detailed information is given by
+
+ man adjust
+ man anomaly
+ man check
+ man codon-usage
+ man compare-lists
+ man generate
+ man get-len
+ man run-glimmer2
+ man get-putative
Added: projects/med/tags/0.13/menu/bio/hmmer.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/hmmer.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+Hmmer: Biological sequence analysis using profile hidden Markov models
+
+Some information about Hmmer from the Debian-Med project.
+
+ Hmmer is a suite of programs which use profile hidden Markov models
+ (profile HMMs) to model the primary structure consensus of a family of
+ protein or nucleic acid sequences.
+
+Homepage: http://hmmer.wustl.edu/
+
+You can get a good overview by the main manpage:
+
+ man hmmer
+
+The Hmmer users guide is available at
+
+ http://localhost/doc/hmmer/hmmer-html/index.html
Added: projects/med/tags/0.13/menu/bio/loki.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/loki.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+Loki: MCMC linkage analysis on general pedigrees
+
+Some information about Loki from the Debian-Med project.
+
+ Performs Markov chain Monte Carlo multipoint linkage analysis on large,
+ complex pedigrees. The current package supports analyses on quantitative
+ traits only, although this restriction will be lifted in later versions.
+ Joint estimation of QTL number, position and effects uses Reversible Jump
+ MCMC. It is also possible to perform affected only IBD sharing analyses.
+
+ Homepage: http://loki.homeunix.net.
+
+You can get a good overview by the main manpage:
+
+ man loki
+
+It is suggested to install the loki-doc package.
Added: projects/med/tags/0.13/menu/bio/mipe.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/mipe.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,44 @@
+Tools to store PCR-derived data
+
+Some information about mipe from the Debian-Med project.
+
+ MIPE provides a standard format to exchange and/or storage of all
+ information associated with PCR experiments using a flat text file. This will:
+ * allow for exchange of PCR data between researchers/laboratories
+ * enable traceability of the data
+ * prevent problems when submitting data to dbSTS or dbSNP
+ * enable the writing of standard scripts to extract data (e.g. a
+ list of PCR primers, SNP positions or haplotypes for different animals)
+
+ Although this tool can be used for data storage, it's primary focus
+ should be data exchange. For larger reporisitories, relational databases
+ are more appropriate for storage of these data. The MIPE format could
+ then be used as a standard format to import into and/or export from
+ these databases.
+
+Homepage: http://mipe.sourceforge.net
+
+You should also read the relevant man pages:
+
+ man mipe06to07
+ man mipe08to09
+ man mipe0_9to1_0
+ man mipe2dbSTS
+ man mipe2fas
+ man mipe2html
+ man mipe2pcroverview
+ man mipe2pcrprimers
+ man mipe2putativesbeprimers
+ man mipe2sbeprimers
+ man mipe2snps
+ man mipeCheckSanity
+ man removePcrFromMipe
+ man removeSbeFromMipe
+ man sbe2mipe
+ man snp2mipe
+ man snpPosOnDesign
+ man snpPosOnSource
+ man csv2mipe
+ man genotype2mipe
+ man mipe2genotypes
+ man removeSnpFromMipe
Added: projects/med/tags/0.13/menu/bio/molphy.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/molphy.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+Some information about MolPhy from the Debian-Med project.
+
+Molphy is an extensive set of tools for MOLecular PHYlogenetics. You can
+get a first overview by the two manpages
+
+ man protml
+ man mollist
+
+For further reading the files in
+
+ /usr/share/doc/molphy
+
+are suggested. Moreover you can find several examples in
+
+ /usr/share/doc/molphy/examples/tests/
+
+which contains a makefile to give you an idea how to call the MolPhy tools.
Added: projects/med/tags/0.13/menu/bio/muscle.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/muscle.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,39 @@
+Multiple alignment program of protein sequences
+
+Some information about Muscle from the Debian-Med project.
+
+MUSCLE is a multiple alignment program for protein sequences. MUSCLE
+stands for multiple sequence comparison by log-expectation. In the
+authors tests, MUSCLE achieved the highest scores of all tested
+programs on several alignment accuracy benchmarks, and is also one of
+the fastest programs out there.
+
+Homepage: http://www.drive5.com/muscle
+
+Basic usage
+
+ muscle -in <inputfile> -out <outputfile>
+
+Common options (for a complete list please see the User Guide):
+
+ -in <inputfile> Input file in FASTA format (default stdin)
+ -out <outputfile> Output alignment in FASTA format (default stdout)
+ -diags Find diagonals (faster for similar sequences)
+ -maxiters <n> Maximum number of iterations (integer, default 16)
+ -maxhours <h> Maximum time to iterate in hours (default no limit)
+ -maxmb <m> Maximum memory to allocate in Mb (default 80% of RAM)
+ -html Write output in HTML format (default FASTA)
+ -msf Write output in GCG MSF format (default FASTA)
+ -clw Write output in CLUSTALW format (default FASTA)
+ -clwstrict As -clw, with 'CLUSTAL W (1.81)' header
+ -log[a] <logfile> Log to file (append if -loga, overwrite if -log)
+ -quiet Do not write progress messages to stderr
+ -stable Output sequences in input order (default is -group)
+ -group Group sequences by similarity (this is the default)
+ -version Display version information and exit
+
+Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
+Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
+Fastest possible (nucleotides): -maxiters 1 -diags
+
+See also: man muscle
Added: projects/med/tags/0.13/menu/bio/ncbi-epcr.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/ncbi-epcr.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,16 @@
+NCBI-EPCR: Tool to test a DNA sequence for the presence of sequence tagged sites
+
+Some information about NCBI-Tools-Bin from the Debian-Med project.
+
+ Electronic PCR feature to test a DNA sequence for the presence of
+ sequence tagged sites. e-PCR looks for STSs in DNA sequences by
+ searching for subsequences that closely match the PCR primers and have
+ the correct order, orientation, and spacing that they could plausibly
+ prime the amplification of a PCR product of the correct molecular weight
+ (Schuler, Genome Research 7:541-50, 1997).
+
+ Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi
+
+ For further information try:
+
+ man e-PCR
Added: projects/med/tags/0.13/menu/bio/ncbi-tools-bin.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/ncbi-tools-bin.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,43 @@
+# The lot of entries just blast the menu to much
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2asn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2ff" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2ff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2gb" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2gb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2xml" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asn2xml" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asndhuff" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="asndhuff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/checksub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="checksub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/debruijn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="debruijn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/entrcmd" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="entrcmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fa2htgs" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="fa2htgs" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastamerge" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="fastamerge" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/findspl" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="findspl" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gbseqget" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="gbseqget" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getfeat" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getfeat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getmesh" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getmesh" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getpub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="getpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gil2bin" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="gil2bin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/idfetch" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="idfetch" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/indexpub" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="indexpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makeset" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="makeset" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/tbl2asn" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="tbl2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/vecscreen" needs="X11" \
+ section="Med/Biology/ncbi-tools-bin" title="vecscreen" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/0.13/menu/bio/ncbi-tools-x11.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/ncbi-tools-x11.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,14 @@
+?package(ncbi-tools-x11):command="/usr/bin/Cn3D-3.0" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Cn3D-3.0" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/Nentrez" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Entrez" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/Psequin" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Sequin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/ddv" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="ddv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/entrez2" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="entrez2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/netentcf" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="Entrez net config" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
+?package(ncbi-tools-x11):command="/usr/bin/udv" needs="X11" \
+ section="Med/Biology/ncbi-tools-x11" title="udv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"
Added: projects/med/tags/0.13/menu/bio/phylip.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/phylip.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,26 @@
+Some information about Phylip from the Debian-Med project.
+
+ A package of programs for inferring phylogenies.
+
+ The PHYLogeny Inference Package is a package of programs for inferring
+ phylogenies (evolutionary trees) from sequences.
+ Methods that are available in the package include parsimony, distance
+ matrix, and likelihood methods, including bootstrapping and consensus
+ trees. Data types that can be handled include molecular sequences, gene
+ frequencies, restriction sites, distance matrices, and 0/1 discrete
+ characters.
+
+If you call phylip in a text console you get some help:
+
+ Usage: /usr/bin/phylip <program>
+ Existing programs are:
+ clique dnacomp dnamlk dollop drawtree kitsch penny retree
+ consense dnadist dnamove dolmove factor mix protdist seqboot
+ contml dnainvar dnapars dolpenny fitch move protpars
+ contrast dnaml dnapenny drawgram gendist neighbor restml
+
+which is quite the same information as the Debian manpage of phylip
+contains.
+There is extensive documentation at /usr/share/doc/phylip and some
+examples in the examples dir at this location.
+
\ No newline at end of file
Added: projects/med/tags/0.13/menu/bio/poa.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/poa.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,18 @@
+Partial Order Alignment for multiple sequence alignment
+
+Some information about t-coffee from the Debian-Med project.
+
+ POA is Partial Order Alignment, a fast program for multiple sequence
+ alignment (MSA) in bioinformatics. Its advantages are speed,
+ scalability, sensitivity, and the superior ability to handle branching
+ / indels in the alignment. Partial order alignment is an approach to
+ MSA, which can be combined with existing methods such as progressive
+ alignment. POA optimally aligns a pair of MSAs and which therefore can
+ be applied directly to progressive alignment methods such as CLUSTAL.
+ For large alignments, Progressive POA is 10-30 times faster than
+ CLUSTALW. POA is published in Bioinformatics. 2004 Jul
+ 10;20(10):1546-56.
+
+See also: man poa
+
+Homepage: http://www.bioinformatics.ucla.edu/poa
Added: projects/med/tags/0.13/menu/bio/r-cran-qtl.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/r-cran-qtl.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,23 @@
+r-cran-qtl: GNU R package for genetic marker linkage analysis
+
+Some information about r-cran-qtl from the Debian-Med project.
+
+ R/qtl is an extensible, interactive environment for
+ mapping quantitative trait loci (QTLs) in experimental crosses. It is
+ implemented as an add-on-package for the freely available and widely used
+ statistical language/software R (see http://www.r-project.org). The
+ user will benefit from the seamless integration of the QTL mapping
+ software into a general statistical analysis program.
+
+ The current version of R/qtl includes facilities for estimating
+ genetic maps, identifying genotyping errors, and performing single-QTL
+ genome scans and two-QTL, two-dimensional genome scans, by interval
+ mapping (with EM algorithm), Haley-Knott regression, and multiple
+ imputation. All of this may be done in the presence of covariates
+ (such as sex, age or treatment). The fit of higher-order QTL models,
+ with sophisticated techniques for model comparisons and model search,
+ will be incorporated soon.
+
+More information can be found at
+
+ Homepage: http://www.biostat.jhsph.edu/~kbroman/qtl/index.html
Added: projects/med/tags/0.13/menu/bio/readseq.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/readseq.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+ReadSeq: Conversion between sequence formats
+
+Some information about readseq from the Debian-Med project.
+
+ Reads and writes nucleic/protein sequences in various formats. Data
+ files may have multiple sequences. Readseq is particularly useful as it
+ automatically detects many sequence formats, and converts between them.
+
+Please read the manual for this program by
+
+ man readseq
+
+To test the program you could also test the examples under
+
+ /usr/share/doc/readseq/tests
+
+using the provided Makefile.
Added: projects/med/tags/0.13/menu/bio/sim4.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/sim4.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,25 @@
+Tool for aligning cDNA and genomic DNA
+
+Some information about sim4 from the Debian-Med project.
+
+ sim4 is a similarity-based tool for aligning an expressed DNA sequence
+ (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end
+ matches when the two input sequences overlap at one end (i.e., the start of
+ one sequence overlaps the end of the other).
+
+ sim4 employs a blast-based technique to first determine the basic matching
+ blocks representing the "exon cores". In this first stage, it detects all
+ possible exact matches of W-mers (i.e., DNA words of size W) between the two
+ sequences and extends them to maximal scoring gap-free segments. In the
+ second stage, the exon cores are extended into the adjacent as-yet-unmatched
+ fragments using greedy alignment algorithms, and heuristics are used to favor
+ configurations that conform to the splice-site recognition signals (GT-AG,
+ CT-AC). If necessary, the process is repeated with less stringent parameters
+ on the unmatched fragments.
+
+
+Homepage: http://www.bx.psu.edu/miller_lab/
+
+Please read the man page of this project:
+
+ man sim4
Added: projects/med/tags/0.13/menu/bio/t-coffee.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/bio/t-coffee.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+Multiple Sequence Alignment
+
+Some information about t-coffee from the Debian-Med project.
+
+ T-Coffee is a multiple sequence alignment package. Given a set of
+ sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+ alignment. Version 2.00 and higher can mix sequences and structures.
+
+ T-Coffee allows the combination of a collection of multiple/pairwise,
+ global or local alignments into a single model. It also allows to
+ estimate the level of consistency of each position within the new
+ alignment with the rest of the alignments. See the pre-print for more
+ information
+
+See also: man t_coffee
+
+Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
Added: projects/med/tags/0.13/menu/cms/zope-zms.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/cms/zope-zms.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,24 @@
+zope-zms: Content management for science, technology and medicine
+
+Some information about Zope ZMS from the Debian-Med project.
+
+ ZMS (Zope based Content Management for Science, Technology and Medicine)
+ is a ready to use solution for efficient electronic publishing. An easy
+ to handle graphical user interface for editors and flexible modelling
+ features (multiple languages, Metadata, content objects, XML
+ import/export, workflow etc.) allow an optimum of productivity: A
+ basic configuration to start with can be created with a few mouse clicks.
+
+ ZMS is perfectly suitable for hospitals, research institutions, NGOs
+ and small to medium-size international companies.
+
+ The ZMS concept is based on a consulting approach for the rational
+ publishing on the internet: the professional user is able to pursue
+ a consequently efficiency oriented producing base with the ZMS software
+ and can hereby also achieve important economic results in the so-called
+ low budget area. The modulation possibilities of the ZMS components and
+ the experienced producing steps makes out of ZMS an incomparable fast tool.
+
+ Homepage: http://www.zms-publishing.com/
+
+ Read /usr/share/doc/zope-zms/README.Debian for the first steps.
Added: projects/med/tags/0.13/menu/imaging-dev/ctn-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging-dev/ctn-dev.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,15 @@
+CTN Development: CTN-Dicom support
+
+Some information about ctn from the Debian-Med project.
+
+The ctn package provides runtime files for Central Test Node,
+a DICOM implementation.
+DICOM is the standard for image storage, annotation, and networking.
+It is used widely for medical imaging.
+
+This is the development package.
+
+For further information have a look into the extensive documentation
+which is in the Debian package ctn-doc.
+
+The homepage is http://www.erl.wustl.edu/DICOM/ctn.html.
Added: projects/med/tags/0.13/menu/imaging-dev/libgtkimreg-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging-dev/libgtkimreg-dev.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+Imreg Development: Image Sequences Development Support
+
+Some information about libgtkimreg-dev from the Debian-Med project.
+
+Please read
+
+ man gtkimreg
+ man gtkimmov
+
+for a detailed description for cutting and moving sets of images.
+A complex example of the usage of these libraries is the image viewer
+paul.
Added: projects/med/tags/0.13/menu/imaging-dev/libmdc2-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging-dev/libmdc2-dev.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,13 @@
+MedCon Development: Medical Image Conversion development
+
+Some information about libmdc-dev from the Debian-Med project.
+
+We are sorry that we can not present a more detailed description to this
+development package. We suggest further reading at the xmedcon homepage
+
+ http://xmedcon.sourceforge.net
+
+because it belongs to the XMedCon package.
+
+The following manpages might help you in getting started:
+ xmedcon-config medcon m-gif m-inw m-acr m-ecat m-anlz m-intf
Added: projects/med/tags/0.13/menu/imaging-dev/libminc0-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging-dev/libminc0-dev.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+MINC Development: MNI medical image format development
+
+Some information about libminc0-dev from the Debian-Med project.
+
+The best way to get started with this development package is to read
+
+ http://localhost/doc/libminc0-dev/
+
+if you have a working webserver installed on your local machine or just
+browse
+
+ /usr/share/doc/libminc0-dev
Added: projects/med/tags/0.13/menu/imaging/ctn.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging/ctn.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,25 @@
+CTN: Runtime files for Central Test Node, a DICOM implementation
+
+Some information about ctn from the Debian-Med project.
+
+The ctn package provides runtime files for Central Test Node,
+a DICOM implementation.
+DICOM is the standard for image storage, annotation, and networking.
+It is used widely for medical imaging.
+
+Information about the tools which are provided can be obtained by
+
+ man dcm_ctnto10
+ man dcm_diff
+ man dcm_dump_element
+ man dcm_dump_file
+ man dcm_make_object
+ man dcm_map_to_8
+ man dcm_rm_element
+ man dcm_verify
+ man dcm_add_fragments
+ man dcm_create_object
+
+The homepage is http://www.erl.wustl.edu/DICOM/ctn.html.
+
+Extensive documentation is provided in the Debian package ctn-doc.
Added: projects/med/tags/0.13/menu/imaging/dcmtk.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging/dcmtk.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,58 @@
+The OFFIS DICOM toolkit command line utilities
+
+Some information about dcmtk from the Debian-Med project.
+
+ DCMTK includes a collection of libraries and applications for examining,
+ constructing and converting DICOM image files, handling offline media,
+ sending and receiving images over a network connection, as well as
+ demonstrative image storage and worklist servers.
+
+Homepage: http://dicom.offis.de/
+
+The package contains a set of utilities. They are described in the
+relevant man pages which are:
+
+ man dbregimg
+ man dcm2pnm
+ man dcm2xml
+ man dcmcjpeg
+ man dcmconv
+ man dcmcrle
+ man dcmdjpeg
+ man dcmdrle
+ man dcmdspfn
+ man dcmdump
+ man dcmftest
+ man dcmgpdir
+ man dcmj2pnm
+ man dcmmkcrv
+ man dcmmkdir
+ man dcmmklut
+ man dcmodify
+ man dcmp2pgm
+ man dcmprscp
+ man dcmprscu
+ man dcmpschk
+ man dcmpsmk
+ man dcmpsprt
+ man dcmpsrcv
+ man dcmpssnd
+ man dcmquant
+ man dcmscale
+ man dcmsign
+ man dcod2lum
+ man dconvlum
+ man dsr2html
+ man dsr2xml
+ man dsrdump
+ man dump2dcm
+ man echoscu
+ man findscu
+ man imagectn
+ man movescu
+ man storescp
+ man storescu
+ man ti
+ man wlmscpfs
+ man xml2dcm
+ man xml2dsr
Added: projects/med/tags/0.13/menu/imaging/medcon.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging/medcon.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+MedCon: MEDical image (DICOM, ECAT, ...) CONversion tool
+
+Some information about medcon from the Debian-Med project.
+
+The homepage is at
+
+ http://xmedcon.sourceforge.net
+
+There exists a xmedcon tool which provides a nice graphical interface
+and might be a good start for beginners.
+
+Alternatively you can type
+
+ man medcon
+
+to learn how to use medcon.
+
Added: projects/med/tags/0.13/menu/imaging/minc-tools.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging/minc-tools.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,29 @@
+MINC Tools: MNI medical image format tools
+
+Some information about minc-tools from the Debian-Med project.
+
+ The Minc file format is a highly flexible medical image file format
+ built on top of the NetCDF generalized data format. The format is
+ simple, self-describing, extensible, portable and N-dimensional, with
+ programming interfaces for both low-level data access and high-level
+ volume manipulation. On top of the libraries is a suite of generic
+ image-file manipulation tools. The format, libraries and tools are
+ designed for use in a medical-imaging research environment : they are
+ simple and powerful and make no attempt to provide a pretty interface
+ to users.
+
+The best way to start using minc-tools is to read the document
+
+ /usr/share/doc/minc-tools/GETTING_STARTED
+
+A reasonable resource of information is
+
+ http://www.nmr.mgh.harvard.edu/~rhoge/minc/
+
+The following manpages are available for the MINC tools suite:
+
+ mincaverage minccalc mincconcat minccopy mincdiff mincedit mincexpand
+ mincextract mincheader mincinfo mincmakescalar mincmakevector mincmath
+ mincresample mincreshape mincstats invert_raw_image mincview mincwindow
+ rawtominc xfmconcat xfminvert voxeltoworld minc_modify_header minclookup
+ minctoraw transformtags worldtovoxel
Added: projects/med/tags/0.13/menu/imaging/nifti-bin.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/imaging/nifti-bin.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,17 @@
+Tool for reading and writing NIfTI-1 MRI and fMRI brain images
+
+Some information about nifti-bin from the Debian-Med project.
+
+ Niftilib is a set of i/o libraries for reading and writing files in the
+ NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical
+ image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI)
+ brain images.
+
+Please read:
+ man nifti_tool
+ man nifti_stats
+ man nifti1_test
+
+Further reading:
+ http://niftilib.sourceforge.net/
+ http://nifti.nimh.nih.gov/
Added: projects/med/tags/0.13/menu/physics/octave.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/physics/octave.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,4 @@
+?package(octave2.1):needs="text" \
+ section="Med/Physics" \
+ title="Octave (2.1)" \
+ command="/usr/bin/octave2.1"
Added: projects/med/tags/0.13/menu/physics/r-base.menu
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/physics/r-base.menu Sat Aug 11 15:42:18 2007
@@ -0,0 +1,4 @@
+?package(r-base-core):needs="text" \
+ section="Med/Physics" \
+ title="GNU R" \
+ command="/usr/bin/R"
Added: projects/med/tags/0.13/menu/tools/mencal.txt
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/menu/tools/mencal.txt Sat Aug 11 15:42:18 2007
@@ -0,0 +1,10 @@
+MenCal: Menstruation Calendar
+
+Some information about mencal from the Debian-Med project.
+
+Please read
+
+ man mencal
+
+for a detailed description of options and the configuration file of the
+menstruation calendar. It is intended to be called from a text console.
Added: projects/med/tags/0.13/tasks/bio
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/bio Sat Aug 11 15:42:18 2007
@@ -0,0 +1,36 @@
+Task: Biology
+Description: Debian-Med micro-biology packages
+ This meta package will install Debian packages related to molecular biology,
+ structural biology and bioinformatics for use in life sciences. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing these.
+
+
+Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle, treeviewx
+Why: Phylogenetic analysis.
+Depends: molphy, phylip, treetool
+Why: Phylogenetic analysis (Non-free, thus only suggested).
+
+Depends: fastlink, loki, r-cran-qtl
+Why: Genetics.
+
+Depends: amap-align, blast2, boxshade, dialign, gff2aplot, hmmer, kalign, mummer, muscle, poa, probcons, proda, \
+ seaview, sim4, sibsim4, sigma-align, t-coffee, wise
+Why: Sequence alignments and related programs.
+Depends: arb, clustalw | clustalw-mpi, clustalx
+Why Sequence alignments and related programs (Non-free, thus only suggested).
+
+Depends: adun.app, garlic, gdpc, ghemical, gromacs, pymol, rasmol
+Why: Molecular modelling and molecular modelling.
+
+Recommends: textopo
+Why: This is only recommended to not necessarily flood the system with TeX packages - perhaps target for -doc?
+
+Depends: biosquid, gff2ps, mipe, melting, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, primer3, readseq, tigr-glimmer
+Why: Tools for the molecular biologist.
+
+Suggests: mozilla-biofox
+Why: Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user.
+
+Suggests: bugsx
+Why: Other packages (Non-free, thus only suggested).
Added: projects/med/tags/0.13/tasks/bio-dev
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/bio-dev Sat Aug 11 15:42:18 2007
@@ -0,0 +1,16 @@
+Task: Biology Development
+Description: Debian-Med packages for development of micro-biology applications
+ This meta package will install Debian packages which might be helpful
+ for development of applications for micro-biological research. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing these.
+
+Depends: bioperl, libncbi6-dev, mcl
+Suggests: biomode, r-base-core
+
+Recommends: libvibrant6-dev
+Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install libmotif-dev it must be possible to deinstall libvibrant6-dev without beeing forced to deinstall med-bio-dev as well
+
+Depends: python-biopython
+
+Depends: libbio-ruby
Added: projects/med/tags/0.13/tasks/cms
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/cms Sat Aug 11 15:42:18 2007
@@ -0,0 +1,9 @@
+Task: Content Management
+Description: Debian-Med content management systems
+ This meta package will install packages which are useful to build a
+ content management system for medical care. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing
+ these.
+
+Depends: zope-zms
Added: projects/med/tags/0.13/tasks/imaging
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/imaging Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+Task: Imaging
+Description: Debian-Med imaging packages
+ This meta package will install Debian packages which might be useful in medical
+ image processing. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing these.
+
+Depends: ctsim, ctn, minc-tools, medcon, xmedcon, dcmtk
+Recommends: pngquant, paul
+Suggests: imagemagick
+
+Depends: libfslio0, libniftiio0, nifti-bin, dicomnifti
Added: projects/med/tags/0.13/tasks/imaging-dev
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/imaging-dev Sat Aug 11 15:42:18 2007
@@ -0,0 +1,12 @@
+Task: Imaging Development
+Description: Debian-Med packages for medical image development
+ This meta package will install Debian packages which might be useful
+ for developing applications for medical image processing. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing these.
+
+Depends: libgtkimreg-dev, ctn-dev, libminc0-dev, libmdc2-dev
+
+Depends: libfslio0-dev, libniftiio0-dev
+
+Suggests: libnifti-doc
Added: projects/med/tags/0.13/tasks/pharmacy
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/pharmacy Sat Aug 11 15:42:18 2007
@@ -0,0 +1,9 @@
+Task: Pharmacy
+Description: Debian-Med packages for pharmaceutical research
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ pharmaceutical research. Please note that there also recommended
+ and only suggested packages which are not installed in any circumstance
+ but only if the user asks for installing these.
+
+Depends: chemtool
Added: projects/med/tags/0.13/tasks/physics
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/physics Sat Aug 11 15:42:18 2007
@@ -0,0 +1,22 @@
+Task: Physics
+Description: Debian-Med packages for medical physicists
+ This meta package contains dependencies for a
+ collection of software and documentation which is useful for
+ medical physicists in radiation oncology, diagnostics imaging
+ and related fields. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing
+ these.
+
+Depends: paw++
+Why: Just depend from the user friendly version because it is easier to \
+ povide a menu item
+Recommends: paw
+Why: This is for the purists with exactly the same functionality as paw++
+Suggests: paw-demos
+
+Depends: octave | octave2.1,
+
+Why: "r-base" ist ein Metapaket, und es ist besser da ne Defaultalternative \
+ zu haben. Dirk Eddelbuettel <edd at debian.org>
+Depends: r-base | r-base-core
Added: projects/med/tags/0.13/tasks/practice
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/practice Sat Aug 11 15:42:18 2007
@@ -0,0 +1,7 @@
+Task: Practice
+Description: Debian-Med packages for practice management
+ This meta package contains dependencies for a
+ collection of software which might be helpful for
+ practitioners to manage their practice.
+
+Depends: gnumed-client
Added: projects/med/tags/0.13/tasks/tools
==============================================================================
--- (empty file)
+++ projects/med/tags/0.13/tasks/tools Sat Aug 11 15:42:18 2007
@@ -0,0 +1,11 @@
+Task: Tools
+Description: Debian-Med several tools
+ This meta package will install tools for several purposes in health care.
+ Currently it just depends from mencal. Please note
+ that there also recommended and only suggested packages which are not
+ installed in any circumstance but only if the user asks for installing these.
+
+Depends: mencal, cycle
+
+Suggests: cl-pubmed
+Why: Strong dependency would cost installing a large amount of Common Lisp tools which in most cases is not worth the effort
More information about the Cdd-commits
mailing list