[med-svn] r8600 - in trunk/packages/strap/trunk/debian: . strap strap/usr strap/usr/bin
Christoph Gille
christophgil-guest at alioth.debian.org
Thu Nov 17 23:13:52 UTC 2011
Author: christophgil-guest
Date: 2011-11-17 23:13:51 +0000 (Thu, 17 Nov 2011)
New Revision: 8600
Added:
trunk/packages/strap/trunk/debian/README.Debian
trunk/packages/strap/trunk/debian/changelog
trunk/packages/strap/trunk/debian/compat
trunk/packages/strap/trunk/debian/compileStrap.sh
trunk/packages/strap/trunk/debian/compileStrap.sh~
trunk/packages/strap/trunk/debian/control
trunk/packages/strap/trunk/debian/copyright
trunk/packages/strap/trunk/debian/docs
trunk/packages/strap/trunk/debian/menu
trunk/packages/strap/trunk/debian/rules
trunk/packages/strap/trunk/debian/rules~
trunk/packages/strap/trunk/debian/strap.1
trunk/packages/strap/trunk/debian/strap.debhelper.log
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/
trunk/packages/strap/trunk/debian/strap/usr/
trunk/packages/strap/trunk/debian/strap/usr/bin/
trunk/packages/strap/trunk/debian/strap/usr/bin/strap
Log:
Added: trunk/packages/strap/trunk/debian/README.Debian
===================================================================
--- trunk/packages/strap/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/strap/trunk/debian/README.Debian 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,6 @@
+strap for Debian
+-----------------
+
+<The homepage of Strap is http://www.bioinformatics.org/strap/>
+
+ -- Christoph Gille <christophgil at googlemail.com> Sat, 05 Nov 2011 17:25:47 +0100
Added: trunk/packages/strap/trunk/debian/changelog
===================================================================
--- trunk/packages/strap/trunk/debian/changelog (rev 0)
+++ trunk/packages/strap/trunk/debian/changelog 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,6 @@
+strap (1-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #xxxxxxxxx)
+
+ -- Christoph Gille <christophgil at googlemail.com> Thu, 17 Nov 2011 18:30:16 +0100
+
Added: trunk/packages/strap/trunk/debian/compat
===================================================================
--- trunk/packages/strap/trunk/debian/compat (rev 0)
+++ trunk/packages/strap/trunk/debian/compat 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1 @@
+8
Added: trunk/packages/strap/trunk/debian/compileStrap.sh
===================================================================
--- trunk/packages/strap/trunk/debian/compileStrap.sh (rev 0)
+++ trunk/packages/strap/trunk/debian/compileStrap.sh 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+
+
+mkdir -p $SRC_TMP
+
+CP=.:$TARBALLS/compilationDependencies.jar:
+# Note compilationDependencies.jar contains those classes that are required for compilation but not for runtime.
+# Conditional compilation does not work properly with javac.
+
+for jar in javatar activation commons-codec commons-httpclient commons-logging httpclient httpclient httpcore httpmime; do
+ jf=/usr/share/java/$jar.jar
+ [ -f $jf ] || echo Jar-file not found $jf
+ CP=$CP:$jf
+done
+
+echo Classpath $CP
+echo
+cd $SRC_TMP
+tar -xzf $TARBALLS/strap_1.orig.tar.gz
+cd strap-$VERSION
+echo PWD=$PWD
+SKIP='/metannogen/\|Superimpose_LajollaProtein.java\|ChJv.java\|Flavine.java\|ChAquaScrollBarUI\|StrapMacApplicationListener'
+SRC_FILES=$(find . -name '[A-Z]*.java' | tr ' ' '\n' | grep -v "$SKIP")
+
+javac -cp $CP $SRC_FILES
+NEW_JAR=$TARBALLS/strap-$VERSION.1.jar
+jar -cf $NEW_JAR charite org/apache
+echo NEW_JAR: $NEW_JAR
+
+
+
+
+
Property changes on: trunk/packages/strap/trunk/debian/compileStrap.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/strap/trunk/debian/compileStrap.sh~
===================================================================
--- trunk/packages/strap/trunk/debian/compileStrap.sh~ (rev 0)
+++ trunk/packages/strap/trunk/debian/compileStrap.sh~ 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+
+
+mkdir -p $SRC_TMP/$REPACKED
+
+CP=.:$TARBALLS/compilationDependencies.jar:
+# Note compilationDependencies.jar contains those classes that are required for compilation but not for runtime.
+# Conditional compilation does not work properly with javac.
+
+for jar in javatar activation commons-codec commons-httpclient commons-logging httpclient httpclient httpcore httpmime; do
+ jf=/usr/share/java/$jar.jar
+ [ -f $jf ] || echo Jar-file not found $jf
+ CP=$CP:$jf
+done
+
+echo $CP
+echo
+cd $SRC_TMP/$REPACKED
+SKIP='/metannogen/\|Superimpose_LajollaProtein.java\|ChJv.java\|Flavine.java\|ChAquaScrollBarUI\|StrapMacApplicationListener'
+SRC_FILES=$(find . -name '[A-Z]*.java' | tr ' ' '\n' | grep -v "$SKIP")
+javac -cp $CP $SRC_FILES
+NEW_JAR=$TARBALLS/strap-$VERSION.1.jar
+jar -cf $NEW_JAR charite org/apache
+echo NEW_JAR: $NEW_JAR
+
+
+
+
+
Property changes on: trunk/packages/strap/trunk/debian/compileStrap.sh~
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control (rev 0)
+++ trunk/packages/strap/trunk/debian/control 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,31 @@
+Source: strap
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Christoph Gille <christophgil at googlemail.com>
+Build-Depends: debhelper (>= 8), openjdk-6-jdk | sun-java6-jdk
+Standards-Version: 3.9.2
+Homepage: http://www.bioinformatics.org/strap/
+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/
+
+Package: strap
+Architecture: all
+Depends: openjdk-6-jre | sun-java6-jre, java-wrappers, ${misc:Depends}, gwrite
+Recommends: neobio
+Suggests: texlive-latex-base
+Enhances: clustalw, tm-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 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.
Added: trunk/packages/strap/trunk/debian/copyright
===================================================================
--- trunk/packages/strap/trunk/debian/copyright (rev 0)
+++ trunk/packages/strap/trunk/debian/copyright 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,52 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://www.bioinformatics.org/strap/strap.jar
+Comment: Some files were removed, see the get-orig-source target in ‘debian/rules’.
+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 Software Foundation; either
+ version 2 of the License, or (at your 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: © 2011 Christoph Gille
+License: GPL-3
+# ********************************************************************************
+Files: remote.png color.png tools.png pencil.png scissor.png lock.png hotplug.gif pdf.png rasmol.png hotplug.png plug.png Loaded from
+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'
+# ********************************************************************************
+Files: eye.gif batch.gif notepad.gif
+Source: http://icone.goldenweb.it/index_file/l/en/d2/computer/default.html
+License: Citation from web site "The icons stored within our database are free and downloadable in .ico, .bmp, or .gif format. .... " #
+# ********************************************************************************
+Files: cygwin.gif big_ wikipedia.jpg ensembl.gif firefox.gif jmol.jpg jV.png ncbi*.jpg pfam.png rasmol.png pymol.fig pubmed*.png prodom.png uniprot.gif
+Source: The respective project pages
+License: ???
+# ********************************************************************************
+Files: winzip.gif
+Source: http://www.winzip.com/graphics/winzip_icon_xp.gif
+License: Permission to use this icon in Strap has been granted by E-Mail Fri, January 16, 2009 19:18 from help1 at winzip.com
+********************************************************************************
+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'
+********************************************************************************
\ No newline at end of file
Added: trunk/packages/strap/trunk/debian/docs
===================================================================
--- trunk/packages/strap/trunk/debian/docs (rev 0)
+++ trunk/packages/strap/trunk/debian/docs 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1 @@
+doc/
Added: trunk/packages/strap/trunk/debian/menu
===================================================================
--- trunk/packages/strap/trunk/debian/menu (rev 0)
+++ trunk/packages/strap/trunk/debian/menu 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,7 @@
+?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"
Added: trunk/packages/strap/trunk/debian/rules
===================================================================
--- trunk/packages/strap/trunk/debian/rules (rev 0)
+++ trunk/packages/strap/trunk/debian/rules 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,44 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+VERSION := 1
+SRC_TMP := $(shell mktemp --tmpdir --directory strap-build.XXXXXXXXXX)
+REPACKED := strap-$(VERSION)
+TARBALLS := $(CURDIR)/../tarballs
+
+%:
+ dh $@
+
+TARBALLS := $(CURDIR)/../tarballs
+DEP_JAR := $(TARBALLS)/compilationDependencies.jar
+CP := .:$(DEP_JAR):/usr/share/java/javatar.jar:/usr/share/java/activation.jar:/usr/share/java/commons-codec.jar:/usr/share/java/commons-httpclient.jar:/usr/share/java/commons-logging.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpclient.jar:/usr/share/java/httpcore.jar:/usr/share/java/httpmime.jar
+
+SKIP := /metannogen/\|Superimpose_LajollaProtein.java\|ChJv.java\|Flavine.java\|ChAquaScrollBarUI\|StrapMacApplicationListener
+
+override_dh_auto_build:
+ dh_auto_build
+ echo xxxxxxxxxxxxxxxxxxxxxxxxxxxx '$(SRC_TMP)'
+ find . -name "*.java" | tr ' ' '\n' | grep -v '$(SKIP)' > ../javaFiles.txt
+ javac -cp $(CP) $(shell cat ../javaFiles.txt )
+ echo "Main-Class: charite.christo.strap.Strap"> Manifest
+ jar -cmf Manifest strap-$(VERSION).jar charite org*
+
+override_dh_clean:
+ dh_clean
+
+SRC_TMP := $(shell mktemp --tmpdir --directory strap-build.XXXXXXXXXX)
+ORIG_JAR := $(SRC_TMP)/strap_$(VERSION).jar
+REPACKED := strap-$(VERSION)
+
+get-orig-source:
+ [ -f $(ORIG_JAR) ] || wget -q -O $(ORIG_JAR) http://www.bioinformatics.org/strap/debian/strap.jar
+ [ -f $(DEP_JAR) ] || wget -q -O $(DEP_JAR) http://www.bioinformatics.org//strap/debian/compilationDependencies.jar
+ rm -rf $(SRC_TMP)/$(REPACKED)
+ mkdir $(SRC_TMP)/$(REPACKED)
+ cd $(SRC_TMP)/$(REPACKED) && unzip -q $(ORIG_JAR) && find . -name "*.class"-delete
+ [ -d $(TARBALLS) ] || mkdir $(TARBALLS)
+ cd $(SRC_TMP) && GZIP="--best --no-name" tar -czf $(TARBALLS)/strap_$(VERSION).orig.tar.gz $(REPACKED)
+ rm -rf $(SRC_TMP)
\ No newline at end of file
Property changes on: trunk/packages/strap/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/strap/trunk/debian/rules~
===================================================================
--- trunk/packages/strap/trunk/debian/rules~ (rev 0)
+++ trunk/packages/strap/trunk/debian/rules~ 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+VERSION := 1
+SRC_TMP := $(shell mktemp --tmpdir --directory strap-build.XXXXXXXXXX)
+REPACKED := strap-$(VERSION).orig
+TARBALLS := $(CURDIR)/../tarballs
+
+%:
+ ./debian/compileStrap.sh
+ dh $@
+
+override_dh_auto_build:
+# dh_auto_build
+
+override_dh_clean:
+ dh_clean
+
+
+
+get-orig-source:
+ ./debian/get-orig-source.sh
+
Property changes on: trunk/packages/strap/trunk/debian/rules~
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/strap/trunk/debian/strap/usr/bin/strap
===================================================================
--- trunk/packages/strap/trunk/debian/strap/usr/bin/strap (rev 0)
+++ trunk/packages/strap/trunk/debian/strap/usr/bin/strap 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,33 @@
+#! /bin/sh
+
+echo '\033[42m\033[37m'$0'\033[0m '
+echo "See http://3d-alignment.eu/ "
+echo
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size
+xmx=-Xmx200M
+CP=/usr/share/strap-base/strap.jar
+for i in $*; do
+ if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+ if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi
+
+
+
+echo The maximum heap size option is $xmx. To change,
+echo add a program line option like -Xmx500M which means a heap size of 500 Megabytes.
+echo
+
+EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -probeWebProxy -stdout -askUpload $*"
+
+echo
+echo $EXEC
+echo
+exec $EXEC
+
+
Property changes on: trunk/packages/strap/trunk/debian/strap/usr/bin/strap
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/strap/trunk/debian/strap.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap.1 (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.1 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,289 @@
+.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\-showScriptText\fR
+
+ Displays the script defined with the -script option.
+
+\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\-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.
+
+.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)
Added: trunk/packages/strap/trunk/debian/strap.debhelper.log
===================================================================
--- trunk/packages/strap/trunk/debian/strap.debhelper.log (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.debhelper.log 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,52 @@
+dh_auto_configure
+dh_auto_build
+dh_auto_build
+dh_auto_test
+dh_prep
+dh_installdirs
+dh_auto_install
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
+dh_auto_build
Added: trunk/packages/strap/trunk/debian/strap.desktop
===================================================================
--- trunk/packages/strap/trunk/debian/strap.desktop (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.desktop 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,11 @@
+[Desktop Entry]
+Version=2.0
+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 3D-Alignments of proteins
Added: trunk/packages/strap/trunk/debian/strap.install
===================================================================
--- trunk/packages/strap/trunk/debian/strap.install (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.install 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,4 @@
+# data usr/lib/strap
+debian/bin/strap usr/bin
+../../tarballs/strap-*.jar usr/lib/strap
+debian/strap.desktop usr/share/applications
Added: trunk/packages/strap/trunk/debian/strap.links
===================================================================
--- trunk/packages/strap/trunk/debian/strap.links (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.links 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1,2 @@
+usr/bin/strap usr/bin/strap-protein-alignment
+usr/share/man/man1/strap.1 usr/share/man/man1/strap-protein-alignment.1
Added: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages (rev 0)
+++ trunk/packages/strap/trunk/debian/strap.manpages 2011-11-17 23:13:51 UTC (rev 8600)
@@ -0,0 +1 @@
+debian/*1
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