[med-svn] r11111 - trunk/packages/strap/trunk/debian
Christoph Gille
christophgil-guest at alioth.debian.org
Wed May 30 21:38:07 UTC 2012
Author: christophgil-guest
Date: 2012-05-30 21:38:07 +0000 (Wed, 30 May 2012)
New Revision: 11111
Removed:
trunk/packages/strap/trunk/debian/menu
trunk/packages/strap/trunk/debian/strap-protein-alignment.1
trunk/packages/strap/trunk/debian/strap.desktop
trunk/packages/strap/trunk/debian/strap.install
trunk/packages/strap/trunk/debian/strap.links
trunk/packages/strap/trunk/debian/strap.manpages
trunk/packages/strap/trunk/debian/strap.postrm
Modified:
trunk/packages/strap/trunk/debian/changelog
trunk/packages/strap/trunk/debian/control
trunk/packages/strap/trunk/debian/rules
Log:
Modified: trunk/packages/strap/trunk/debian/changelog
===================================================================
--- trunk/packages/strap/trunk/debian/changelog 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/changelog 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,6 +1,6 @@
strap (1-1) UNRELEASED; urgency=low
- * Initial release (Closes: #xxxxxxxxx)
+ * Initial release (Closes: #675202)
-- Christoph Gille <christophgil at googlemail.com> Thu, 17 Nov 2011 18:30:16 +0100
Modified: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/control 2012-05-30 21:38:07 UTC (rev 11111)
@@ -11,21 +11,23 @@
Package: strap
Architecture: all
-Depends: strap-base, ${misc:Depends}, gwrite, catdoc, clustalw, tm-align, pymol, texlive-latex-base, mustang
-Recommends:
+Depends: strap-base, ${misc:Depends}, gwrite, catdoc, clustalw, kalign, tm-align, pymol, texlive-latex-base, mustang
+Recommends: muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align
Suggests:
-Enhances: clustalw, tm-align, pymol, mustang
-Description: Compute and edit Sequence and structure alignments of proteins.
- Strap is a work-bench for proteins. It can compute multiple sequence
- alignments and structure alignments and it is used structure/function
- prediction and database searching. Modern standard tools can be used
- in an intuitive graphical user interface which follows the paradigms
- of modern user interfaces such as drag'n drop. The sequence
- alignment view and the 3D-visualization (Pymol, Jmol or OpenAstex)
- are tightly linked. Information can be attached to residue
- selections such as free text notes as well as 3D and 1D display
- styles. Figures can be created in publication quality. The alignment
- can be exported in several formats: PDF, MS-Word, HTML, Jalview,
- Multiple-Fasta, ClustalW, MSF, HSSP - see http://3d-alignment.eu/ for
- details. Interactive alignments can be published in Web-pages. For
- this purpose, HTML code is generated automatically.
+Enhances: clustalw, tm-align, pymol, mustang, muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align
+Description: Compute and edit Sequence and structure alignments of
+ proteins. Strap is a work-bench for proteins. It can compute
+ multiple sequence alignments and structure alignments and it is used
+ for structure/function prediction and database searching. Modern
+ standard tools can be used in an intuitive graphical user interface
+ which follows the paradigms of modern user interfaces such as drag'n
+ drop. The sequence alignment view and the 3D-visualization (Pymol,
+ Jmol or OpenAstex) are tightly linked. Information can be attached
+ to residue selections such as free text notes as well as 3D and 1D
+ display styles. Figures can be created in publication quality. The
+ alignment can be exported in several formats: PDF, MS-Word, HTML,
+ Jalview, Multiple-Fasta, ClustalW, MSF, HSSP - see
+ http://3d-alignment.eu/ for details. Interactive alignments can be
+ published in Web-pages. For this purpose, HTML code is generated
+ automatically. Strap is scriptable and can be used by programs and
+ web-services to display sequence alignments and 3D-superpositions.
Deleted: trunk/packages/strap/trunk/debian/menu
===================================================================
--- trunk/packages/strap/trunk/debian/menu 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/menu 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,7 +0,0 @@
-?package(strap):\
- needs="X11"\
- section="Applications/Science/Biology"\
- hints="Sequence alignment"\
- longtitle="Strap: User Interface for sequence and 3D protein alignments"\
- title="Strap"\
- command="/usr/bin/strap-protein-alignment"
Modified: trunk/packages/strap/trunk/debian/rules
===================================================================
--- trunk/packages/strap/trunk/debian/rules 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/rules 2012-05-30 21:38:07 UTC (rev 11111)
@@ -7,17 +7,4 @@
%:
dh $@
-MANFILE1 := ~/java/charite/christo/strap/strap-protein-alignment.1
-
-override_dh_auto_build:
- test -f $(MANFILE1) && cp $(MANFILE1) debian/strap-protein-alignment.1
-
-override_dh_clean:
- dh_clean
-
-get-orig-source:
- echo get-orig-source - do nothing
-
-
-
Deleted: trunk/packages/strap/trunk/debian/strap-protein-alignment.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap-protein-alignment.1 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap-protein-alignment.1 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,304 +0,0 @@
-.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]
-
-.B strap-protein-alignment [\fIalignment_files\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 with a leading \fB@\fR sign or 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 File Compression
-
-The following file compression methods are 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 text
-
-\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 class name of a dialog is the tab-text can be obtained by opening the help text.
-
-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. Assume there are 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.
-
-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 for DAS servers that are
-
-\fB\-s3d\fR=\fIJavaClass\fR
-
-Sets the Java class to superimpose proteins.
-
-A short 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\-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.
-
-This setting influences the result of searches in growing
-databases. For example consider the similarity search method
-Blast. With the cache turned on, Strap would present a previously
-computed Blast result even though new sequences might have been
-published since last run.
-
-\fB\-keepFiles\fR
-
-Do not delete temp-files after the session. This is only important for
-debugging.
-
-\fB\-Xmx500m\fR
-
-This is an option of the java command and not of Strap.
-It sets the heap size to 500 Megabyte.
-
-\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'n 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\-toMultipleFasta\fR or \fB\-toClustal\fR or \fB\-toFasta\fR \fIProtein or alignment files\fR
-
-Loads the proteins and generates protein or ungapped multiple sequence
-files with the respective format. The file paths are written to
-stdout. The program terminates.
-
-.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 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 1999-2011
-
-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)
-.BR openastex (1)
-.BR strap-text-viewer (1)
Deleted: trunk/packages/strap/trunk/debian/strap.desktop
===================================================================
--- trunk/packages/strap/trunk/debian/strap.desktop 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap.desktop 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,11 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Name=Strap protein alignments
-Exec=/usr/bin/strap-protein-alignment
-Terminal=false
-# Icon=
-Type=Application
-MimeType=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;
-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 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap.install 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,2 +0,0 @@
-debian/bin/strap-protein-alignment usr/bin
-debian/strap.desktop usr/share/applications
Deleted: trunk/packages/strap/trunk/debian/strap.links
===================================================================
--- trunk/packages/strap/trunk/debian/strap.links 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap.links 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,2 +0,0 @@
-usr/share/man/man1/strap-protein-alignment.1 usr/share/man/man1/strap.1
-usr/bin/strap-protein-alignment usr/bin/strap
Deleted: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap.manpages 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1 +0,0 @@
-debian/strap-protein-alignment.1
Deleted: trunk/packages/strap/trunk/debian/strap.postrm
===================================================================
--- trunk/packages/strap/trunk/debian/strap.postrm 2012-05-30 19:57:42 UTC (rev 11110)
+++ trunk/packages/strap/trunk/debian/strap.postrm 2012-05-30 21:38:07 UTC (rev 11111)
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-if [ -x "`which update-menus 2>/dev/null`" ]; then update-menus ; fi
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