[med-svn] [fastml] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Wed Nov 18 17:30:24 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fastml.
commit 6b917648ffe31274418c9098be7ba889b3674c43
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 18 18:29:29 2015 +0100
Initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 32 ++++++++++++++++++++++++++++++++
debian/copyright | 12 ++++++++++++
debian/rules | 13 +++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 33 +++++++++++++++++++++++++++++++++
debian/watch | 3 +++
8 files changed, 100 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..57b24e0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+fastml (3.1-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Mon, 22 Jun 2015 09:47:25 +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..39656a5
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,32 @@
+Source: fastml
+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)
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastml.git
+Vcs-Git: git://anonscm.debian.org/debian-med/fastml.git
+Homepage: http://fastml.tau.ac.il/
+
+Package: fastml
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: maximum likelihood ancestral amino-acid sequence reconstruction
+ FastML is a bioinformatics tool for the reconstruction of ancestral
+ sequences based on the phylogenetic relations between homologous
+ sequences. FastML runs several algorithms that reconstruct the ancestral
+ sequences with emphasis on an accurate reconstruction of both indels and
+ characters. For character reconstruction the previously described FastML
+ algorithms are used to efficiently infer the most likely ancestral
+ sequences for each internal node of the tree. Both joint and the
+ marginal reconstructions are provided. For indels reconstruction the
+ sequences are first coded according to the indel events detected within
+ the multiple sequence alignment (MSA) and then a state-of-the-art
+ likelihood model is used to reconstruct ancestral indels states. The
+ results are the most probable sequences, together with posterior
+ probabilities for each character and indel at each sequence position for
+ each internal node of the tree. FastML is generic and is applicable for
+ any type of molecular sequences (nucleotide, protein, or codon
+ sequences).
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e7e6784
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,12 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: FastML
+Upstream-Contact: Haim Ashkenazy <haim.ashkenazy at gmail.com>
+Source: http://fastml.tau.ac.il/source.php#download
+
+Files: *
+Copyright: 1996-2014 Tal Pupko <talp at post.tau.ac.il>
+License: GPL-2
+
+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..a9e420a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f libs/phylogeny/make.dep \
+ programs/fastml/make.dep \
+ programs/gainLoss/make.dep \
+ programs/indelCoder/make.dep
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..d98083d
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,33 @@
+Reference:
+ - Author: Haim Ashkenazy and Osnat Penn and Adi Doron-Faigenboim and Ofir Cohen and Gina Cannarozzi and Oren Zomer and Tal Pupko
+ Title: "FastML: a web server for probabilistic reconstruction of ancestral sequences"
+ Journal: Nucleic Acids Research
+ Year: 2012
+ Volume: 40
+ Number: Web Server issue
+ Pages: W580–W584
+ DOI: 10.1093/nar/gks498
+ PMID: 22661579
+ URL: http://nar.oxfordjournals.org/content/40/W1/W580
+ eprint: http://nar.oxfordjournals.org/content/40/W1/W580.full.pdf+html
+ - Author: Tal Pupko and Itsik Peer and Masami Hasegawa and Dan Graur and Nir Friedman
+ Title: "A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families"
+ Journal: Bioinformatics
+ Year: 2002
+ Volume: 18
+ Number: 8
+ DOI: 10.1093/bioinformatics/18.8.1116
+ Pages: 1116-23
+ PMID: 12176835
+ URL: http://bioinformatics.oxfordjournals.org/content/18/8/1116.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/18/8/1116.full.pdf+html
+ - Author: Tal Pupko and Itsik Peer†and Ron Shamir and Dan Graur
+ Title: "A fast algorithm for joint reconstruction of ancestral amino acid sequences"
+ Journal: Molecular Biology and Evolution
+ Year: 2000
+ Volume: 17
+ Number: 6
+ Pages: 890-6
+ PMID: 10833195
+ URL: http://mbe.oxfordjournals.org/content/17/6/890.full
+ eprint: http://mbe.oxfordjournals.org/content/17/6/890.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..d29663a
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://fastml.tau.ac.il/source.php source/FastML.v([\d.]*)\.tgz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastml.git
More information about the debian-med-commit
mailing list