[med-svn] r12815 - in trunk/packages/strap/trunk/debian: . source
Christoph Gille
christophgil-guest at alioth.debian.org
Mon Jan 21 22:14:18 UTC 2013
Author: christophgil-guest
Date: 2013-01-21 22:14:18 +0000 (Mon, 21 Jan 2013)
New Revision: 12815
Added:
trunk/packages/strap/trunk/debian/source/
trunk/packages/strap/trunk/debian/source/format
trunk/packages/strap/trunk/debian/watch
Removed:
trunk/packages/strap/trunk/debian/strap.desktop
trunk/packages/strap/trunk/debian/strap.install
trunk/packages/strap/trunk/debian/strap.manpages
trunk/packages/strap/trunk/debian/strap.png
trunk/packages/strap/trunk/debian/strap.xpm
trunk/packages/strap/trunk/debian/strap_protein_alignment.1
Modified:
trunk/packages/strap/trunk/debian/changelog
trunk/packages/strap/trunk/debian/compat
trunk/packages/strap/trunk/debian/control
trunk/packages/strap/trunk/debian/copyright
trunk/packages/strap/trunk/debian/rules
Log:
Simplification: Moved several files to the upstream tgz. Moved installation logic from debian/rules to the upstream Makefile.
Modified: trunk/packages/strap/trunk/debian/changelog
===================================================================
--- trunk/packages/strap/trunk/debian/changelog 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/changelog 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,4 +1,4 @@
-strap (1) UNRELEASED; urgency=low
+strap (1-1) UNRELEASED; urgency=low
* Initial release (Closes: #675202)
Modified: trunk/packages/strap/trunk/debian/compat
===================================================================
--- trunk/packages/strap/trunk/debian/compat 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/compat 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/control 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,10 +1,10 @@
Source: strap
Section: science
-Priority: extra
+Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Christoph Gille <christophgil at googlemail.com>
-Build-Depends: debhelper (>= 8), strap-base, texlive-latex-extra
-Standards-Version: 3.9.1
+Build-Depends: debhelper (>= 9), strap-base, texlive-latex-extra
+Standards-Version: 3.9.4
Homepage: http://3d-alignment.eu/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/strap/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/strap/trunk/
Modified: trunk/packages/strap/trunk/debian/copyright
===================================================================
--- trunk/packages/strap/trunk/debian/copyright 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/copyright 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,453 +1,446 @@
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
+Source: http://www.bioinformatics.org/strap/debian/
Files: debian/*
Copyright: © 2011 Christoph Gille
License: GPL-3
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+ % of this license or (at your option) any later version.
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+ .
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+ yourself.
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+ this is not the case (e.g., if a few lines of code are reused for a
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+ Important Recommendations
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+ Defining What Constitutes the Work
+ .
+ The LPPL requires that distributions of the Work contain all the
+ files of the Work. It is therefore important that you provide a
+ way for the licensee to determine which files constitute the Work.
+ This could, for example, be achieved by explicitly listing all the
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+ in that place. In the absence of an unequivocal list it might be
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+
\ No newline at end of file
Modified: trunk/packages/strap/trunk/debian/rules
===================================================================
--- trunk/packages/strap/trunk/debian/rules 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/rules 2013-01-21 22:14:18 UTC (rev 12815)
@@ -7,12 +7,9 @@
%:
dh $@
-D := $(CURDIR)/debian
-L := /usr/share/texmf-texlive/tex/latex
+TARBALLS := $(CURDIR)/../tarballs
-override_dh_auto_build:
- dh_auto_build
- # Only two small sty files of the huge package texlive-latex-extra are required in Strap
- # Include these two files such that texlive-latex-extra can be ommitted
- cat $L/texshade/texshade.sty > $D/texshade.sty
- cat $L/vmargin/vmargin.sty > $D/vmargin.sty
+
+get-orig-source:
+ mkdir -p $(TARBALLS)
+ uscan --verbose --force-download --repack --rename --destdir=$(TARBALLS)
Added: trunk/packages/strap/trunk/debian/source/format
===================================================================
--- trunk/packages/strap/trunk/debian/source/format (rev 0)
+++ trunk/packages/strap/trunk/debian/source/format 2013-01-21 22:14:18 UTC (rev 12815)
@@ -0,0 +1 @@
+3.0 (quilt)
Deleted: trunk/packages/strap/trunk/debian/strap.desktop
===================================================================
--- trunk/packages/strap/trunk/debian/strap.desktop 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/strap.desktop 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,11 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Name=Strap protein alignments
-Exec=/usr/bin/strap_protein_alignment -stdout=false
-Terminal=false
-Icon=strap
-Type=Application
-MimeType=text/x-clustalw-alignment; text/x-stockholm-alignment; chemical/seq-aa-fasta;chemical/x-pdb;application/x-mfa;chemical/x-nexus;chemical/x-swissprot;chemical/seq-na-genbank;application/x-gp;chemical/seq-aa-genpept;text/x-strap-script;
-Categories=Education;Science;Chemistry;
-GenericName=Strap protein alignments
-Comment=Sequence and structure alignments of proteins
Deleted: trunk/packages/strap/trunk/debian/strap.install
===================================================================
--- trunk/packages/strap/trunk/debian/strap.install 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/strap.install 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,8 +0,0 @@
-debian/texshade.sty usr/lib/strap
-debian/vmargin.sty usr/lib/strap
-debian/bin/strap_protein_alignment usr/bin
-debian/strap.desktop usr/share/applications
-
-debian/*.desktop usr/share/applications/
-debian/strap.png usr/share/pixmaps/
-debian/strap.xpm usr/share/pixmaps/
Deleted: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/strap.manpages 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,2 +0,0 @@
-
-debian/strap_protein_alignment.1
\ No newline at end of file
Deleted: trunk/packages/strap/trunk/debian/strap.png
===================================================================
(Binary files differ)
Deleted: trunk/packages/strap/trunk/debian/strap.xpm
===================================================================
--- trunk/packages/strap/trunk/debian/strap.xpm 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/strap.xpm 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,40 +0,0 @@
-/* XPM */
-static char *strap[] = {
-/* columns rows colors chars-per-pixel */
-"32 32 2 1",
-" c #000000",
-". c None",
-/* pixels */
-"................................",
-"................................",
-"................................",
-"................................",
-"................................",
-"... ...",
-"... ...",
-"................................",
-"................................",
-"................................",
-"........... ...",
-"........... ...",
-"................................",
-"................................",
-"................................",
-"....... ...",
-"....... ...",
-"................................",
-"................................",
-"................................",
-".............. ...",
-".............. ...",
-"................................",
-"................................",
-"................................",
-"..... ...",
-"..... ...",
-"................................",
-"................................",
-"................................",
-"................................",
-"................................"
-};
Deleted: trunk/packages/strap/trunk/debian/strap_protein_alignment.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2013-01-21 00:30:08 UTC (rev 12814)
+++ trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2013-01-21 22:14:18 UTC (rev 12815)
@@ -1,377 +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.
-
-
-.SH Synopsis
-
-.B strap_protein_alignment [\fIprotein_files\fR] [\fIalignment_files\fR]
-
-.B strap_protein_alignment -script=[\fIURL or File or named pipe\fR]
-
-.B strap_protein_alignment -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
-
-.B strap_protein_alignment
-[\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_protein_alignment [\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)
-
Added: trunk/packages/strap/trunk/debian/watch
===================================================================
--- trunk/packages/strap/trunk/debian/watch (rev 0)
+++ trunk/packages/strap/trunk/debian/watch 2013-01-21 22:14:18 UTC (rev 12815)
@@ -0,0 +1,6 @@
+# watch control file for uscan
+version=3
+http://www.bioinformatics.org/strap/debian/strap_([0-9.]+).orig\.tar\.gz debian uupdate
+
+
+
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