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