[med-svn] [prottest] 02/02: Add initial packaging

[Andreas Tille]

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

tille pushed a commit to branch master
in repository prottest.

commit 78c4189f5ebe9878a82cc360d283b3f30b977591
Author: Andreas Tille <tille at debian.org>
Date:   Sun Sep 6 08:23:11 2015 +0200

    Add initial packaging
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 33 +++++++++++++++++++++++++++++++++
 debian/copyright         | 19 +++++++++++++++++++
 debian/rules             | 15 +++++++++++++++
 debian/source/format     |  1 +
 debian/upstream/metadata | 12 ++++++++++++
 debian/watch             |  4 ++++
 8 files changed, 90 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..8f28a28
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+prottest (3.4+dfsg-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #?????)
+
+ -- Andreas Tille <tille at debian.org>  Sat, 05 Sep 2015 00:35:44 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..b9312fd
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,33 @@
+Source: prottest
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               alter-sequence-alignment,
+               libbetter-appframework-java,
+               libmtj-java,
+               libpal-java
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/prottest.git
+Vcs-Git: git://anonscm.debian.org/debian-med/prottest.git
+Homepage: http://code.google.com/p/prottest3/
+
+Package: prottest
+Architecture: all
+Depends: ${java:Depends},
+         ${misc:Depends}
+Description: Selection of best-fit models of protein evolution
+ PROTTEST (ModelTest's relative) is a program for selecting the model of
+ protein evolution that best fits a given set of sequences (alignment).
+ This java program is based on the Phyml program (for maximum likelihood
+ calculations and optimization of parameters) and uses the PAL library as
+ well. Models included are empirical substitution matrices (such as WAG,
+ LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
+ MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
+ replacement, and specific improvements (+I:invariable sites, +G: rate
+ heterogeneity among sites, +F: observed amino acid frequencies) to
+ account for the evolutionary constraints impossed by conservation of
+ protein structure and function. ProtTest uses the Akaike Information
+ Criterion (AIC) and other statistics (AICc and BIC) to find which of the
+ candidate models best fits the data at hand.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..3f21c08
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,19 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Prottest
+Upstream-Contact: David Posada <dposada at uvigo.es>
+Source: http://cs.njit.edu/usman/probalign/
+Files-Excluded: lib/alter.jar
+                lib/appframework-1.0.3.jar
+                lib/mpj.jar
+                lib/pal.jar
+
+Files: *
+Copyright: 2008-2014 David Posada <dposada at uvigo.es>
+License: GPL-2+
+
+++ -> see THIRDPARTYLICENSES file
+
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-2+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..97e018e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,15 @@
+#!/usr/bin/make -f
+# debian/rules for prottest
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+	dh $@ --with javahelper
+
+get-orig-source:
+	uscan --verbose --force-download --repack --compression xz
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..c524d6b
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Diego Darriba and Guillermo L. Taboada and Ramón Doallo and David Posada
+  Title: "ProtTest 3: fast selection of best-fit models of protein evolution"
+  Journal: Bioinformatics
+  Year: 2011
+  Volume: 27
+  Number: 8
+  Pages: 1164-5
+  DOI: 10.1093/bioinformatics/btr088
+  PMID: 21335321
+  URL: http://bioinformatics.oxfordjournals.org/content/early/2011/02/17/bioinformatics.btr088
+  eprint: http://bioinformatics.oxfordjournals.org/content/early/2011/02/17/bioinformatics.btr088.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..dd95464
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+   https://github.com/ddarriba/prottest3/releases .*/archive/(\d[\d.-]+)-release\.(?:tar(?:\.gz|\.bz2)?|tgz)

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