[med-svn] r11110 - in trunk/packages/strap-base/trunk/debian: . bin
Christoph Gille
christophgil-guest at alioth.debian.org
Wed May 30 19:57:43 UTC 2012
Author: christophgil-guest
Date: 2012-05-30 19:57:42 +0000 (Wed, 30 May 2012)
New Revision: 11110
Added:
trunk/packages/strap-base/trunk/debian/bin/
trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment
trunk/packages/strap-base/trunk/debian/postrm
trunk/packages/strap-base/trunk/debian/strap-base.desktop
trunk/packages/strap-base/trunk/debian/strap-base.links
trunk/packages/strap-base/trunk/debian/strap-base.manpages
trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1
Removed:
trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment
Modified:
trunk/packages/strap-base/trunk/debian/rules
trunk/packages/strap-base/trunk/debian/strap-base.install
Log:
Deleted: trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap-protein-alignment 2012-05-28 20:35:57 UTC (rev 11055)
+++ trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment 2012-05-30 19:57:42 UTC (rev 11110)
@@ -1,34 +0,0 @@
-#! /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/lib/java/strap-protein-alignment-1.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 $xmx.
-echo To change, add a program line option like -Xmx500M
-echo which would set heap size to 500 Megabytes.
-echo
-
-EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload $*"
-
-echo
-echo $EXEC
-echo
-$EXEC
-
-
Copied: trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment (from rev 11105, trunk/packages/strap/trunk/debian/bin/strap-protein-alignment)
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1,34 @@
+#! /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/lib/strap-base/strap-protein-alignment-1.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 $xmx.
+echo To change, add a program line option like -Xmx500M
+echo which would set heap size to 500 Megabytes.
+echo
+
+EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=kalign -probeWebProxy -stdout -askUpload $*"
+
+echo
+echo $EXEC
+echo
+$EXEC
+
+
Copied: trunk/packages/strap-base/trunk/debian/postrm (from rev 11056, trunk/packages/strap/trunk/debian/postrm)
===================================================================
--- trunk/packages/strap-base/trunk/debian/postrm (rev 0)
+++ trunk/packages/strap-base/trunk/debian/postrm 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1,3 @@
+# Automatically added by dh_installmenu
+if [ -x "`which update-menus 2>/dev/null`" ]; then update-menus ; fi
+# End automatically added section
Modified: trunk/packages/strap-base/trunk/debian/rules
===================================================================
--- trunk/packages/strap-base/trunk/debian/rules 2012-05-30 19:32:22 UTC (rev 11109)
+++ trunk/packages/strap-base/trunk/debian/rules 2012-05-30 19:57:42 UTC (rev 11110)
@@ -12,12 +12,14 @@
SRC_TMP := $(HOME)/tmp/build_strap-base
TARBALLS := $(CURDIR)/../tarballs
ORIG_TAR=$(TARBALLS)/strap-base_$(VERSION).orig.tar.gz
+MANFILE1 := ~/java/charite/christo/strap/strap-protein-alignment.1
override_dh_installdocs:
dh_installdocs
override_dh_auto_build:
+ test -f $(MANFILE1) && cp $(MANFILE1) debian/strap-protein-alignment.1
cd $(SRC_TMP) && tar -xzf $(ORIG_TAR)
# Native program to manage GUI frames by frame title. It provides always-on-top, iconization, to-front etc.
cd $(SRC_TMP)/src && cc -lm -lX11 -o $(CURDIR)/nativeTools_unix2 nativeTools_unix2.c
Copied: trunk/packages/strap-base/trunk/debian/strap-base.desktop (from rev 11105, trunk/packages/strap/trunk/debian/strap.desktop)
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.desktop (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap-base.desktop 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1,11 @@
+[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
Modified: trunk/packages/strap-base/trunk/debian/strap-base.install
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.install 2012-05-30 19:32:22 UTC (rev 11109)
+++ trunk/packages/strap-base/trunk/debian/strap-base.install 2012-05-30 19:57:42 UTC (rev 11110)
@@ -1,2 +1,4 @@
strap-protein-alignment-1.jar usr/lib/strap-base
nativeTools_unix2 usr/lib/strap-base
+debian/bin/strap-protein-alignment usr/bin
+debian/strap-base.desktop usr/share/applications
Copied: trunk/packages/strap-base/trunk/debian/strap-base.links (from rev 11106, trunk/packages/strap/trunk/debian/strap.links)
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.links (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap-base.links 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1,2 @@
+usr/share/man/man1/strap-protein-alignment.1 usr/share/man/man1/strap.1
+usr/bin/strap-protein-alignment usr/bin/strap
Copied: trunk/packages/strap-base/trunk/debian/strap-base.manpages (from rev 11055, trunk/packages/strap/trunk/debian/strap.manpages)
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.manpages (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap-base.manpages 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1 @@
+debian/strap-protein-alignment.1
Copied: trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1 (from rev 11055, trunk/packages/strap/trunk/debian/strap-protein-alignment.1)
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1 2012-05-30 19:57:42 UTC (rev 11110)
@@ -0,0 +1,304 @@
+.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)
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