Author: alteholz Date: 2013-05-02 17:49:18 +0000 (Thu, 02 May 2013) New Revision: 13470
Added: trunk/packages/proalign/trunk/debian/proalign.1 trunk/packages/proalign/trunk/debian/proalign.manpages Modified: trunk/packages/proalign/trunk/debian/changelog trunk/packages/proalign/trunk/debian/control trunk/packages/proalign/trunk/debian/rules trunk/packages/proalign/trunk/debian/scripts/proalign Log: ready for upload Modified: trunk/packages/proalign/trunk/debian/changelog =================================================================== --- trunk/packages/proalign/trunk/debian/changelog 2013-05-02 17:09:17 UTC (rev 13469) +++ trunk/packages/proalign/trunk/debian/changelog 2013-05-02 17:49:18 UTC (rev 13470) @@ -1,4 +1,4 @@ -proalign (0.603-1) UNRELEASED; urgency=low +proalign (0.603-1) unstable; urgency=low * Initial release (Closes: #378290) Modified: trunk/packages/proalign/trunk/debian/control =================================================================== --- trunk/packages/proalign/trunk/debian/control 2013-05-02 17:09:17 UTC (rev 13469) +++ trunk/packages/proalign/trunk/debian/control 2013-05-02 17:49:18 UTC (rev 13470) @@ -5,7 +5,8 @@ DM-Upload-Allowed: yes Uploaders: Andreas Tille <ti...@debian.org>, Thorsten Alteholz <deb...@alteholz.de> -Build-Depends: debhelper (>= 9) +Build-Depends: debhelper (>= 9), + default-jdk Standards-Version: 3.9.4 Homepage: http://ueg.ulb.ac.be/ProAlign/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/ @@ -13,7 +14,8 @@ Package: proalign Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, ${misc:Depends}, + default-jre Description: Probabilistic multiple alignment program ProAlign performs probabilistic sequence alignments using hidden Markov models (HMM). It includes a graphical interface (GUI) allowing to (i) Added: trunk/packages/proalign/trunk/debian/proalign.1 =================================================================== --- trunk/packages/proalign/trunk/debian/proalign.1 (rev 0) +++ trunk/packages/proalign/trunk/debian/proalign.1 2013-05-02 17:49:18 UTC (rev 13470) @@ -0,0 +1,79 @@ +.TH PROALIGN "1" "May 2013" "ProAlign" "User Commands" +.SH NAME +proalign \- a probabilistic multiple alignment program +.SH SYNOPSIS +.B proalign [OPTIONS] +.SH DESCRIPTION +Only limited usage of the program is possible from command line. +Better use version with GUI (start without OPTIONS). +.SH OPTIONS +.TP +\fB\-nogui\fR +force command line +.TP +\fB-seqfile=<sequence file>\fR +.TP +\fB-treefile=<tree file>\fR +.TP +\fB-newtree \fR +compute a new guide tree +.TP +\fB-sample \fR +sample traceback path; if not given, Viterbi is chosen +.TP +\fB-delta=<HMM delta> or \-delta=estimate \fR +if not given, default is used +.TP +\fB-epsilon=<HMM epsilon> or \-epsilon=estimate \fR +if not given, default is used +.TP +\fB-gapfreq=<gap frequency> \fR +if not given, default is used +.TP +\fB-gapprob=<gap substitution probability> \fR +if not given, default is used +.TP +\fB-bwidth=<search band width> \fR +if not given, default is used +.TP +\fB-distscale=<distance scale factor> \fR +for branch lengths +.TP +\fB-nocorrection \fR +no correction for pairwise distances on guide tree computation +.TP +\fB-notrailing \fR +no trailing sequence corrcection +.TP +\fB-trailing=<trailing sequence correction length> \fR +for missing ends +.TP +\fB-penalize=true, or =false \fR +penalize end gaps on pairwise alignments for guide tree +.TP +\fB-writemean \fR +write mean posterior probability of sites +.TP +\fB-writeall \fR +write posterior probability of each node +.TP +\fB-writeroot \fR +write root node character probabilities +.TP +\fB-wag \fR +use WAG probability table +.TP +\fB-dayhoff \fR +use Dayhoff probability table +.TP +\fB-jtt \fR +use JTT probability table +.TP +\fB-outfile=<alignment file>\fR +.TP +\fB\-outformat=pir, \-outformat=msf, \-outformat=phylip, or \-outformat=nexus \fR +output format +.TP +\fB-quiet \fR +no log + Added: trunk/packages/proalign/trunk/debian/proalign.manpages =================================================================== --- trunk/packages/proalign/trunk/debian/proalign.manpages (rev 0) +++ trunk/packages/proalign/trunk/debian/proalign.manpages 2013-05-02 17:49:18 UTC (rev 13470) @@ -0,0 +1 @@ +debian/proalign.1 Modified: trunk/packages/proalign/trunk/debian/rules =================================================================== --- trunk/packages/proalign/trunk/debian/rules 2013-05-02 17:09:17 UTC (rev 13469) +++ trunk/packages/proalign/trunk/debian/rules 2013-05-02 17:49:18 UTC (rev 13470) @@ -8,15 +8,9 @@ override_dh_auto_build: mkdir -p build javac -d ./build *.java - find (cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *) #(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class) -override_dh_auto_install: - find - dh_auto_install - #dh_installchangelogs README - get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs Modified: trunk/packages/proalign/trunk/debian/scripts/proalign =================================================================== --- trunk/packages/proalign/trunk/debian/scripts/proalign 2013-05-02 17:09:17 UTC (rev 13469) +++ trunk/packages/proalign/trunk/debian/scripts/proalign 2013-05-02 17:49:18 UTC (rev 13470) @@ -1,5 +1,7 @@ #!/bin/sh +PARA=$@ + if [ -z $JAVA_HOME ]; then java=java else @@ -9,7 +11,7 @@ if [ -x /usr/share/proalign ]; then if [ -r /usr/share/proalign/ProAlign.jar ]; then #cd /usr/share/proalign && $java -jar ProAlign.jar - $java -jar /usr/share/proalign/ProAlign.jar + $java -jar /usr/share/proalign/ProAlign.jar $PARA else echo "Could not find /usr/share/proalign/ProAlign.jar" fi _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit