[med-svn] [proalign] 03/10: ready for upload

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository proalign.

commit 79c050fa5b109fbaaab10da7b842478ea36fefca
Author: Thorsten Alteholz <alteholz at debian.org>
Date:   Thu May 2 17:49:18 2013 +0000

    ready for upload
---
 debian/changelog         |  2 +-
 debian/control           |  6 ++--
 debian/proalign.1        | 79 ++++++++++++++++++++++++++++++++++++++++++++++++
 debian/proalign.manpages |  1 +
 debian/rules             |  6 ----
 debian/scripts/proalign  |  4 ++-
 6 files changed, 88 insertions(+), 10 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 77940b8..f5bb9a3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-proalign (0.603-1) UNRELEASED; urgency=low
+proalign (0.603-1) unstable; urgency=low
 
   * Initial release (Closes: #378290)
 
diff --git a/debian/control b/debian/control
index 8f03506..471c27f 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 DM-Upload-Allowed: yes
 Uploaders: Andreas Tille <tille at debian.org>,
  Thorsten Alteholz <debian at 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 @@ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/
 
 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)
diff --git a/debian/proalign.1 b/debian/proalign.1
new file mode 100644
index 0000000..03304e2
--- /dev/null
+++ b/debian/proalign.1
@@ -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
+
diff --git a/debian/proalign.manpages b/debian/proalign.manpages
new file mode 100644
index 0000000..2958a32
--- /dev/null
+++ b/debian/proalign.manpages
@@ -0,0 +1 @@
+debian/proalign.1
diff --git a/debian/rules b/debian/rules
index 1d3af7e..71d903a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -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
diff --git a/debian/scripts/proalign b/debian/scripts/proalign
index 474feb7..3024912 100644
--- a/debian/scripts/proalign
+++ b/debian/scripts/proalign
@@ -1,5 +1,7 @@
 #!/bin/sh
 
+PARA=$@
+
 if [ -z $JAVA_HOME ]; then
         java=java
 else
@@ -9,7 +11,7 @@ fi
 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

-- 
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