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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Christoph Gille <[email protected]> +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 [email protected] +******************************************************************************** +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
