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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Source: http://fastml.tau.ac.il/source.php#download + +Files: * +Copyright: 1996-2014 Tal Pupko <[email protected]> +License: GPL-2 + +Files: debian/* +Copyright: 2015 Andreas Tille <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
