[med-svn] r12816 - trunk/packages/strap-base/trunk/debian
Christoph Gille
christophgil-guest at alioth.debian.org
Mon Jan 21 22:21:43 UTC 2013
Author: christophgil-guest
Date: 2013-01-21 22:21:43 +0000 (Mon, 21 Jan 2013)
New Revision: 12816
Removed:
trunk/packages/strap-base/trunk/debian/bin/
trunk/packages/strap-base/trunk/debian/etc/
trunk/packages/strap-base/trunk/debian/strap-base.install
trunk/packages/strap-base/trunk/debian/strap-base.links
trunk/packages/strap-base/trunk/debian/strap-base.manpages
trunk/packages/strap-base/trunk/debian/strap_base.1
trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_html.1
trunk/packages/strap-base/trunk/debian/strap_to_msf.1
trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_word.1
Modified:
trunk/packages/strap-base/trunk/debian/copyright
trunk/packages/strap-base/trunk/debian/rules
trunk/packages/strap-base/trunk/debian/watch
Log:
Simplification: Moved several files to the upstream tgz. Moved installation logic from debian/rules to the upstream Makefile.
Modified: trunk/packages/strap-base/trunk/debian/copyright
===================================================================
--- trunk/packages/strap-base/trunk/debian/copyright 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/copyright 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,386 +1,378 @@
Format: http://dep.debian.net/deps/dep5/
Upstream-Name: Strap
Upstream-Contact: Christoph Gille christoph_gi-at-googlemail-com
-Source: http://www.bioinformatics.org/strap/debian/strap-base_1.orig.tar.gz
-Comment: Some files were removed, see the get-orig-source target in ‘debian/rules’.
+Source: http://www.bioinformatics.org/strap/debian/
-Files: * Copyright: © 2011 Christoph Gille License: GPL-3 Strap 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
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-option) any later version. . Strap 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 Strap; if
-not, write to the Free Software Foundation, Inc., 51 Franklin Street,
-Fifth Floor, Boston, MA 02110-1301 USA. . Proper attribution of the
-author as the source of the software would be appreciated. Comment:
-On Debian systems, the complete text of the GNU General Public License
-version 2 can be found in ‘/usr/share/common-licenses/GPL-2’ #
-********************************************************************************
-Files: debian/* Copyright: © 2012 Christoph Gille License: GPL-3 #
-********************************************************************************
+Files: debian/*
+Copyright: © 2011 Christoph Gille
+License: GPL-3
+ Strap 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
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+ Proper attribution of the author as the source of the software would
+ be appreciated. Comment: On Debian systems, the complete text of
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+
+
Files: 3d.gif browser16.gif ledgreen16.gif
Source: http://www.phoca.cz/demo/gallery-categories/category/22-nuvola-icons
-License: LGPL-2.1 Comment: On Debian systems, the complete text of the
-Apache license can be found in '/usr/share/common-licenses/LGPL-2.1' #
-********************************************************************************
+License: LGPL-2.1
+Comment: On Debian systems, the complete text of the Apache license can be found in '/usr/share/common-licenses/Apache*'
+
Files: *.png
Source: http://icons8.com/ http://www.visualpharm.com/
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+Comment: Citation from Web-site: We use the license called Creative
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+ icons are free for personal use and also free for commercial use,
+ but we require linking to our web site. If you don’t want to place a
+ link, purchase them for $99 per set on IconPharm.
-# ********************************************************************************
-File: astex.gif
+Files: astex.gif
Source: http://openastexviewer.net/
License: LPGL
-# ********************************************************************************
-File: jmol.gif
+
+Files: jmol.gif
Source: http://sourceforge.net/projects/jmol/
-License: LGPLv2
-# ********************************************************************************
-File: pfam.gif
+License: LGPL-2
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Source: pfam.sanger.ac.uk/
-License: Creative Commons Zero ("CC0") licence.
-# ********************************************************************************
-File: uniprot.gif
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Source: http://www.uniprot.org
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-# ********************************************************************************
+License: CC-BY-ND
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Files: org/apache/tools/bzip2/*
License: Apache license
- Comment: On Debian systems, the complete text of the Apache license can be found in '/usr/share/common-licenses/Apache-2.0'
-********************************************************************************
+
Files: UncompressInputStream.java
Source: https://jsms.com.br/svn/tags/initial/HTTPClient/UncompressInputStream.java
License: LGPL-3
- Comment: On Debian systems, the complete text of the Apache license can be found in '/usr/share/common-licenses/LGPL'
-********************************************************************************
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Modified: trunk/packages/strap-base/trunk/debian/rules
===================================================================
--- trunk/packages/strap-base/trunk/debian/rules 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/rules 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,32 +1,14 @@
#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
-# export DH_VERBOSE=1
+export DH_VERBOSE=1
-VERSION := 1
-
%:
dh $@
TARBALLS := $(CURDIR)/../tarballs
-ORIG_TAR=$(TARBALLS)/strap-base_$(VERSION).orig.tar.gz
-override_dh_installdocs:
- dh_installdocs
-override_dh_auto_build:
- # Native program to manage GUI frames by frame title.
- #It provides always-on-top, iconization, to-front etc.
- cd src && cc -lm -lX11 -o $(CURDIR)/nativeTools_unix2 nativeTools_unix2.c
- cd src && find . -name "*.java" > ../javaFiles.txt
-
- cd src && javac -O -cp @../classpath.txt @../javaFiles.txt
- cd src && jar -cmf ../Manifest $(CURDIR)/strap-protein-alignment-$(VERSION).jar *
-
-override_dh_clean:
- dh_clean
-
-
get-orig-source:
mkdir -p $(TARBALLS)
uscan --verbose --force-download --repack --rename --destdir=$(TARBALLS)
Deleted: trunk/packages/strap-base/trunk/debian/strap-base.install
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.install 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap-base.install 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,11 +0,0 @@
-strap-protein-alignment-1.jar usr/lib/strap-base
-nativeTools_unix2 usr/lib/strap-base
-
-debian/bin/strap_to_fasta usr/bin
-debian/bin/strap_to_multiple_fasta usr/bin
-debian/bin/strap_to_clustal usr/bin
-debian/bin/strap_to_msf usr/bin
-debian/bin/strap_to_html usr/bin
-debian/bin/strap_to_word usr/bin
-debian/bin/strap_base usr/bin
-debian/etc/bash_completion.d/strap_to_fasta etc/bash_completion.d
Deleted: trunk/packages/strap-base/trunk/debian/strap-base.links
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.links 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap-base.links 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,2 +0,0 @@
-usr/share/man/man1/strap_base.1 usr/share/man/man1/strap.1
-
Deleted: trunk/packages/strap-base/trunk/debian/strap-base.manpages
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.manpages 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap-base.manpages 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,7 +0,0 @@
-debian/strap_base.1
-debian/strap_to_fasta.1
-debian/strap_to_multiple_fasta.1
-debian/strap_to_clustal.1
-debian/strap_to_html.1
-debian/strap_to_word.1
-debian/strap_to_msf.1
Deleted: trunk/packages/strap-base/trunk/debian/strap_base.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,380 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH Strap 1 "October 2011"
-.SH NAME
-
-Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure.
-
-strap_base is intended to be run from other programs which use strap as a viewer.
-Strap users should install the package strap which installs also all required debian packages.
-
-
-.SH Synopsis
-
-.B strap_base [\fIprotein_files\fR] [\fIalignment_files\fR]
-
-.B strap_base -script=[\fIURL or File or named pipe\fR]
-
-.B strap_base -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
-
-.B strap_base
-[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR]
-
-
-.SH DESCRIPTION
-
-The free computer program Strap aligns proteins by sequence and
-3D-structure. Strap supports the simultaneous analysis of hundreds of
-proteins and integrates amino acid sequence, secondary structure,
-3D-structure and genomic- and mRNA-sequence. Using standard methods,
-alignments are computed automatically based on sequence and structure.
-Import and export of single proteins is very easy by Drag-and-Drop.
-
-.SS Home-Page
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-.SH PROGRAM PARAMETERS
-
-.SS Protein/alignment files
-
-Strap can be started with protein files or alignment files as parameters.
-The following formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-If at least one protein file is specified, Strap will choose the
-current working directory as the project directory. Otherwise the
-project directory is requested at the beginning of the session.
-
-
-Files preceded by a \fB@\fR sign are interpreted as lists of files.
-
-\fBCurly parenthesis\fR are used for placing sequences into the same
-alignment row. At the UNIX command prompt, the parentheses need to be
-quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR
-\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR
-would put two proteins into the first and three proteins into the
-second alignment row. If there are more than one sequences in a row,
-only the top most sequence is displayed.
-
-
-.SS Loading of protein entries from remote databases:
-
-The command line options \fB-load="\fR\fI space separated list of
-database entries \fR\fB"\fR loads proteins or alignments given as URL
-or database-colon-id. The option \fB-align="\fR\fI ... \fR\fB"\fR also
-aligns the downloaded proteins.
-
-
-
-.SS File Compression
-
-Supported: .gz, .bz2 and .Z
-
-.SS Parts of proteins
-
-To display only a subset of a protein, a suffix is appended to the
-protein file name.
-Residue subsets are specified by an exclamation mark and a subset
-expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-
-Program options start with a dash. The values \fBtrue\fR and
-\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
-"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
-as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
-equivalent check-box or choice menu in the graphical user interface.
-
-If the Web-start script http://www.bioinformatics.org/strap/strap.php
-is started, the options are given as web-variable without the leading
-dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
-URL.
-
-\fB-help\fR
-
-Prints this manual
-
-\fB-manual\fR
-
-Generates a comprehensive manual for the web browser.
-
-\fB\-noSeqres\fR
-
- Skip SEQRES lines of PDB files.
-
-\fB\-noIdentical\fR
-
-Do not load a sequence identical to an already loaded one.
-
-\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR
-
-Opens a certain dialog at start.
-The Java class name of a dialog is shown in the tool tip of the help button when the shift key is pressed.
-
-Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
-
-\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
-
-Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html.
-Script files in the current directory should be written with a leading
-"./" like "./myScript.txt" since Strap recognizes files by the
-presence of a slash and the absence of white space and colon.
-
-Two or more script files can be given:
--script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
-The optional number suffix defines the order of consecutively executed scripts.
-
-Script commands can be given directly. Consider a few protein files
-in PDB format loaded by Strap. The option
--script="open_3D viewName, *"
-would display all proteins with 3D-coordinates three-dimensionally
-(See -v3d=). Scripts consisting of more than one line should be
-stored in a file and the file path or URL should be given.
-
-If scripts are run on a server which allows many instances simultaneously,
-consider to use a database backend instead of the file based cache for computed results
-(See http://www.bioinformatics.org/strap/cache.html)
-
-
-Example:
-
--script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
-
-\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
-
-Only needed to access unregistered DAS servers.
-
-\fB\-s3d\fR=\fIJavaClass\fR
-
-Sets the Java class for superimposing proteins.
-
-The short name or the full Java class name can be used such as "tm_align" for "Superimpose_TM_align".
-
-Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
-
-\fB\-a3d\fR=\fIJavaClass\fR
-
-Sets the Java class to compute structure based sequence alignments.
-
-Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
-
-\fB\-v3d\fR=\fIJavaClass\fR
-
-Sets the Java class to display 3D-structures.
-
-Example: -v3d=jmol or -v3d=pymol or -v3d=astex
-
-\fB\-aligner2\fR=\fIJavaClass\fR
-
-Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
-Default value is PairAlignerNeoBioPROXY.
-
-Example: -aligner2=MultipleAlignerClustalW
-
-
-\fB\-alignerP\fR=\fIJavaClass\fR
-
-Sets the Java class for aligning sequences and structures.
-The default is clustalW.
-
-Example: -alignerP=t_coffee
-
-
-\fB\-log3d\fR
-
-All 3D-commands which are sent to 3D-protein viewers are printed to stdout.
-
-\fB\-useDebian=false\fR \fB\-useDebian=true\fR
-
-If set to true, use the Debian packages for external programs rather
-than the program versions included in Strap. For example Strap would
-use /usr/bin/pymol instead of downloading and using the Pymol from
-http://www.bioinformatics.org/strap/Binaries/.
-
-\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR
-
-See section Web proxies.
-
-\fB\-noCache\fR
-
-Do not use cached results of previous
-computations. This setting can be changed in the graphical user
-interface with a check-box.
-Also see http://www.bioinformatics.org/strap/cache.html.
-
-\fB\-keepFiles\fR
-
-Do not delete temp-files after the session. This is only important for
-debugging.
-
-
-\fB\-geometry=\fI666x333+11+22\fR
-
-Sets the size and location of the application frame to width 666,
-height 333, horizontal screen position 11 and vertical position 22;
-
-\fB\-laf=\fIlookAndFeel\fR
-
-Examples:
-
--laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
-
--laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
-
--laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
-
--laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
-
-Also non-standard Look-and-Feels can be used. Consider tinylaf which
-can be installed as a Debian package. The following two options would
-apply tinylaf:
-
- \fB-cp=\fR/usr/share/java/tinylaf.jar
--laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
-
-See also http://en.wikipedia.org/wiki/Look_and_feel.
-
-\fB\-toFasta\fR \fIProtein or alignment files\fR
-
-Generates a sequence file in Fasta format for each loaded protein.
-
-.SS Interprocess communication
-
-Strap can be controled from another application using named pipes.
-The -script option does not only take files and URLS but also named
-pipes. Other applications can write script commands to the pipe which
-are then executed by Strap.
-
-
-
-.SS Security
-
-\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
-to remote servers. The user might not want unpublished sequences to be
-sent to servers.
-
-\fB\-askExec\fR[=t/f] The user is asked when an external program is
-executed. Executing native programs might be regarded as security
-risk. There is a positive and a negative list which can be edited in
-the menu "Security" of the Preferences-menu.
-
-\fB\-allowFileModification\fR According to the default policy, files
-are only modified, created or deleted if they reside in the project
-directory or if the file path contains "StrapAlign". This is to
-prevent files to be lost. With this option file modification control
-is deactivated.
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-.SH ALIGNMENT FILE GENERATION
-
-With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or
-\fB\-toMSF\fR or \fB\-toHTML\fR or \fB\-toWord\fR, Strap can be used as a command line
-tool to generate multiple sequence alignment files. The protein or
-alignment files given in the command line are loaded and the output
-file is generated. Finally the program terminates. Prior file export, the
-proteins may be aligned:
-
-.B strap_base [\fIalignment_files\fR] -script="align *" -toMSF
-
-
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-
-
-.SS Residue annotations in HTML alignment output.
-
-Residue positions to be highlighted in the html output need to
-be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
-The script command \fInew_aminoacid_selection\fR is used to create a new
-selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
-used to attach information. The script may also be used to
-define the [gapped] amino acid sequences.
-
-
-.SH PROJECT DIRECTORY
-
-The project directory holds information for gaps, 3D-transformations,
-annotations and exported files. Usually, the protein files are also
-located in the project directory. The project directory path must not
-contain white space, such as "My data" or "Eigene Dateien". Therefore
-the project directory can usually not be located in the home directory
-on Windows-XP.
-
-.SH WEB-PROXY
-
-With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in
-three different ways: (1) Directly, without Web-proxy (2) With the
-settings found in the environment variable http_proxy and (3) using
-the default mechanism of Java to apply the system wide settings. With the
-setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the
-Internet. with the option \fB-sysProxies=t\fR Strap will use the
-Java-built-in mechanism to find the system wide settings, (which might
-not work properly, depending on the Java system).
-
-.SH ALIGNMENT-FILE-EXPORT
-
-Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A
-colorized alignment with highlighted residue selections and secondary
-structure can be exported in HTML and PDF. The colorized HTML output
-can be modified in MS-Word or other text processors. The rendering
-styles of the PDF output can be stored in annotations of residue
-selections.
-
-.SH 3D-VISUALIZATION
-
-The following 3D-protein viewers are tightly linked with the alignment
-view: Pymol, Jmol, OpenAstex. The rendering styles can be stored
-within residue selections. There is a generic Rasmol like scripting
-language which can be applied to all embedded visualization software.
-If the desired effect can not be achieved with this generic commands,
-also specific commands can be associated with residue
-selections.
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-
-A comprehensive manual is created with the option \fB-manual\fR
-
-.BR jalview (1)
-.BR clustalx (1)
-.BR seaview (1)
-.BR boxshade (1)
-.BR pymol (1)
-
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,123 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_clustal 1 "Mai 2012"
-.SH NAME
-strap_to_clustal \- Reads amino acid sequences and creates a multiple sequence alignment file in clustal format.
-
-.SH SYNOPSIS
-
-strap_to_clustal [\fIprotein or alignment files\fR]
-
-strap_to_clustal [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
-
-strap_to_clustal [\fIprotein or alignment files\fR] -script="align *"
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
-A single alignment file with all sequences is created using clustal format
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-\fB-o\fR=\fIoutput-file\fR Specifies an output file
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-\fB-script\fR=\fIscript-line\fR
-\fB-script\fR=\fIfile\fR or
-\fB-script\fR=\fInamed_pipe\fR
-\fB-script\fR=\fIURL\fR
-Each script line starts with a strap command and may be followed by arguments.
-The script is run line by line.
-For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
-Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
-In this case no sequence files need to be given and the align command is not required.
-In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
-the secondary structure to be displayed. This information is provided with script commands.
-See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-
-If computations are performed within the script and if more than one Strap instances are running at the same time,
-then the default file based cache is not applicable and the SQL database based cache should be used.
-This is described in http://www.bioinformatics.org/strap/cache.html.
-
-
-
-
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,65 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_fasta 1 "Mai 2012"
-.SH NAME
-strap_to_fasta \- Reads amino acid sequences and creates a fasta formated sequence file for each sequence.
-
-.SH SYNOPSIS
-
-strap_to_fasta [\fIprotein or alignment files\fR]
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
- For each loaded sequence a fasta file is written.
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_html.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_html.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_html.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,131 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_html 1 "Mai 2012"
-.SH NAME
-strap_to_html \- Reads amino acid sequences and creates an alignment view for web browsers.
-
-.SH SYNOPSIS
-
-strap_to_html [\fIprotein or alignment files\fR]
-
-strap_to_html [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
-
-strap_to_html [\fIprotein or alignment files\fR] -script="align *"
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
-A html file with the rendered alignment is written. It can be viewed in a web browser.
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-\fB-o\fR=\fIoutput-file\fR Specifies an output file
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-\fB-script\fR=\fIscript-line\fR
-\fB-script\fR=\fIfile\fR or
-\fB-script\fR=\fInamed_pipe\fR
-\fB-script\fR=\fIURL\fR
-Each script line starts with a strap command and may be followed by arguments.
-The script is run line by line.
-For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
-Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
-In this case no sequence files need to be given and the align command is not required.
-In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
-the secondary structure to be displayed. This information is provided with script commands.
-See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-
-If computations are performed within the script and if more than one Strap instances are running at the same time,
-then the default file based cache is not applicable and the SQL database based cache should be used.
-This is described in http://www.bioinformatics.org/strap/cache.html.
-
-
-
-.SS Residue annotations in HTML alignment output.
-
-Residue positions to be highlighted in the html output need to
-be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
-The script command \fInew_aminoacid_selection\fR is used to create a new
-selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
-used to attach information. The script may also be used to
-define the [gapped] amino acid sequences.
-
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_msf.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,123 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_msf 1 "Mai 2012"
-.SH NAME
-strap_to_msf \- Reads amino acid sequences and creates a multiple sequence alignment file in msf format.
-
-.SH SYNOPSIS
-
-strap_to_msf [\fIprotein or alignment files\fR]
-
-strap_to_msf [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
-
-strap_to_msf [\fIprotein or alignment files\fR] -script="align *"
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
-A single alignment file with all sequences is created using msf format
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-\fB-o\fR=\fIoutput-file\fR Specifies an output file
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-\fB-script\fR=\fIscript-line\fR
-\fB-script\fR=\fIfile\fR or
-\fB-script\fR=\fInamed_pipe\fR
-\fB-script\fR=\fIURL\fR
-Each script line starts with a strap command and may be followed by arguments.
-The script is run line by line.
-For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
-Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
-In this case no sequence files need to be given and the align command is not required.
-In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
-the secondary structure to be displayed. This information is provided with script commands.
-See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-
-If computations are performed within the script and if more than one Strap instances are running at the same time,
-then the default file based cache is not applicable and the SQL database based cache should be used.
-This is described in http://www.bioinformatics.org/strap/cache.html.
-
-
-
-
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,123 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_multiple_fasta 1 "Mai 2012"
-.SH NAME
-strap_to_multiple_fasta \- Reads amino acid sequences and creates a multiple fast file.
-
-.SH SYNOPSIS
-
-strap_to_multiple_fasta [\fIprotein or alignment files\fR]
-
-strap_to_multiple_fasta [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
-
-strap_to_multiple_fasta [\fIprotein or alignment files\fR] -script="align *"
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
-A single alignment file with all sequences is created using fasta format
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-\fB-o\fR=\fIoutput-file\fR Specifies an output file
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-\fB-script\fR=\fIscript-line\fR
-\fB-script\fR=\fIfile\fR or
-\fB-script\fR=\fInamed_pipe\fR
-\fB-script\fR=\fIURL\fR
-Each script line starts with a strap command and may be followed by arguments.
-The script is run line by line.
-For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
-Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
-In this case no sequence files need to be given and the align command is not required.
-In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
-the secondary structure to be displayed. This information is provided with script commands.
-See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-
-If computations are performed within the script and if more than one Strap instances are running at the same time,
-then the default file based cache is not applicable and the SQL database based cache should be used.
-This is described in http://www.bioinformatics.org/strap/cache.html.
-
-
-
-
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Deleted: trunk/packages/strap-base/trunk/debian/strap_to_word.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_word.1 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/strap_to_word.1 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,131 +0,0 @@
-.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
-.TH strap_to_word 1 "Mai 2012"
-.SH NAME
-strap_to_word \- Reads amino acid sequences and creates an alignment view which can be edited in a word processor.
-
-.SH SYNOPSIS
-
-strap_to_word [\fIprotein or alignment files\fR]
-
-strap_to_word [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
-
-strap_to_word [\fIprotein or alignment files\fR] -script="align *"
-
-
-
-.SH DESCRIPTION
-
-Amino acid sequences are loaded from input files or are defined using
-the scripting languages.
-A doc-file for word processors (MS-Word, gwrite, OpenOffice) is written.
-
-
-
-.SH INPUT FILES
-
-The amino acid sequences are extracted from alignment files and protein files.
-A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-.SS File Compression
-
-Supported are .gz, .bz2 and .Z.
-
-.SS Parts of proteins
-
-To load only a subset of a proteins, a suffix is appended to the name of the
-protein input file. Residue subsets are specified by an exclamation
-mark and a subset expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax
-\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-\fB-o\fR=\fIoutput-file\fR Specifies an output file
-.SS Alignment format
-
-Comma separated display options can be appended directly (!no space) after the output file name.
-
- w=\fIresidues per line\fR Setting output width
-
- r=\fIcolumn range\fR Example: 20-30
-
- r=\fIresidue position range\fR Example: aProtein/10-20
-
-
-
-\fB-script\fR=\fIscript-line\fR
-\fB-script\fR=\fIfile\fR or
-\fB-script\fR=\fInamed_pipe\fR
-\fB-script\fR=\fIURL\fR
-Each script line starts with a strap command and may be followed by arguments.
-The script is run line by line.
-For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
-Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
-In this case no sequence files need to be given and the align command is not required.
-In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
-the secondary structure to be displayed. This information is provided with script commands.
-See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-
-If computations are performed within the script and if more than one Strap instances are running at the same time,
-then the default file based cache is not applicable and the SQL database based cache should be used.
-This is described in http://www.bioinformatics.org/strap/cache.html.
-
-
-
-.SS Residue annotations in HTML alignment output.
-
-Residue positions to be highlighted in the html output need to
-be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
-The script command \fInew_aminoacid_selection\fR is used to create a new
-selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
-used to attach information. The script may also be used to
-define the [gapped] amino acid sequences.
-
-
-
-.SH Parameters for the Java virtual machine
-
-If the java process is started from a script file,
-parameters can be passed directly to the Java command.
-Those parameters need to be prefixed with "JVM_".
-This does not (yet) work for MS-Windows.
-
-
-Examples:
-
-\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
-\fB JVM_-ea\fR Enable assertions
-
-
-
-
-
-
-.SH HOME-PAGE
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2012
-
-License GPL
-
-.SH "SEE ALSO"
-.BR strap_to_clustal (1)
-.BR strap_to_msf (1)
-.BR strap_to_fasta (1)
-.BR strap_to_multiple_fasta (1)
-.BR strap_to_html (1)
-.BR strap_to_word (1)
-.BR strap_protein_alignment (1)
-.BR sequenceconverter (1)
-.BR cdbfasta (1)
-.BR squizz (1)
Modified: trunk/packages/strap-base/trunk/debian/watch
===================================================================
--- trunk/packages/strap-base/trunk/debian/watch 2013-01-21 22:14:18 UTC (rev 12815)
+++ trunk/packages/strap-base/trunk/debian/watch 2013-01-21 22:21:43 UTC (rev 12816)
@@ -1,5 +1,6 @@
# watch control file for uscan
version=3
http://www.bioinformatics.org/strap/debian/strap-base_([0-9.]+).orig\.tar\.gz debian uupdate
+# http://localhost/debian/strap-base_([0-9.]+).orig\.tar\.gz debian uupdate
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