[med-svn] [transit] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Fri Mar 3 13:44:41 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository transit.
commit 67ffd49ceb18e0a59da6a4607e83137378de1660
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 3 14:41:45 2017 +0100
Add initial packaging
---
debian/README.Debian | 7 +++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 38 ++++++++++++++++++++++++++++++++++++++
debian/copyright | 24 ++++++++++++++++++++++++
debian/rules | 13 +++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 3 +++
9 files changed, 104 insertions(+)
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..73991a4
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,7 @@
+transit for Debian
+==================
+
+Due to a name space conflict with the package tpp the tool /usr/bin/tpp
+is renamed to /usr/bin/transit-tpp.
+
+ -- Andreas Tille <tille at debian.org> Fri, 03 Mar 2017 10:50:10 +0100
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7e5a4ec
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+transit (2.0.2-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Fri, 03 Mar 2017 10:50:10 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..cd4c5f0
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,38 @@
+Source: transit
+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 (>= 10),
+ python-all-dev,
+ python-setuptools
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/transit.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/transit.git
+Homepage: http://pythonhosted.org/tnseq-transit/transit_overview.html
+
+Package: transit
+Architecture: any
+Depends: ${python:Depends},
+ ${misc:Depends},
+ python-numpy,
+ python-scipy,
+ python-pillow,
+ python-matplotlib,
+ python-wxgtk3.0
+Description: statistical calculations of essentiality of genes or genomic regions
+ This is a software that can be used to analyze Tn-Seq datasets. It
+ includes various statistical calculations of essentiality of genes or
+ genomic regions (including conditional essentiality between 2
+ conditions). These methods were developed and tested as a collaboration
+ between the Sassetti lab (UMass) and the Ioerger lab (Texas A&M)
+ .
+ TRANSIT is capable of analyzing TnSeq libraries constructed with Himar1
+ or Tn5 datasets.
+ .
+ TRANSIT assumes you have already done pre-processing of raw sequencing
+ files (.fastq) and extracted read counts into a .wig formatted file.
+ The .wig file should contain the counts at all sites where an insertion
+ could take place (including sites with no reads). For Himar1 datasets
+ this is all TA sites in the genome. For Tn5 datasets this would be all
+ nucleotides in the genome.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1b16788
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,24 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: TRANSIT
+Source: https://github.com/mad-lab/transit/releases
+
+Files: *
+Copyright: 2015-2017 Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
+License: GPL-3
+
+Files: debian/*
+Copyright: 2017 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+License: GPL-3
+ TRANSIT is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License.
+ .
+ TRANSIT is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems you can find a copy of the GNU General Public License
+ at /usr/share/common-licenses/GPL-3.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..03ae07f
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+%:
+ dh $@ --with python2
+
+override_dh_install:
+ dh_install
+ mv debian/$(DEBPKGNAME)/usr/bin/tpp debian/$(DEBPKGNAME)/usr/bin/transit-tpp
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..1ce7349
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Michael A. DeJesus and Chaitra Ambadipudi and Richard Baker and Christopher Sassetti and Thomas R. Ioerger
+ Title: "TRANSIT - A Software Tool for Himar1 TnSeq Analysis"
+ Journal: PLOS
+ Year: 2015
+ Volume: 11
+ Number: 10
+ Pages: e1004401
+ DOI: 10.1371/journal.pcbi.1004401
+ PMID: 26447887
+ URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004401
+ eprint: http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004401&type=printable
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..b54e7e6
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+
+https://github.com/mad-lab/transit/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/transit.git
More information about the debian-med-commit
mailing list