[med-svn] [transdecoder] 02/05: initial Debianization
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Feb 13 12:23:10 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository transdecoder.
commit d3dadfa2c032542d1d217ab3f6737d699b68de4c
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Fri Feb 13 06:31:36 2015 -0500
initial Debianization
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 39 +++++++++++++++++++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++++++++++++++
debian/createmanpages | 16 ++++++++++++++++
debian/rules | 23 +++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 5 +++++
9 files changed, 130 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..c8a3e83
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+transdecoder (2.0.1+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Michael R. Crusoe <mcrusoe at msu.edu> Fri, 13 Feb 2015 06:26:24 -0500
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..cf5c0cb
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,39 @@
+Source: transdecoder
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: https://transdecoder.github.io/
+
+Package: transdecoder
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends}
+Description: find coding regions within transcripts
+ TransDecoder identifies candidate coding regions within transcript sequences,
+ such as those generated by de novo RNA-Seq transcript assembly using Trinity,
+ or constructed based on RNA-Seq alignments to the genome using Tophat and
+ Cufflinks.
+ .
+ TransDecoder identifies likely coding sequences based on the following
+ criteria:
+ .
+ a minimum length open reading frame (ORF) is found in a transcript sequence
+ .
+ a log-likelihood score similar to what is computed by the GeneID software is
+ > 0.
+ .
+ the above coding score is greatest when the ORF is scored in the 1st reading
+ frame as compared to scores in the other 5 reading frames.
+ .
+ if a candidate ORF is found fully encapsulated by the coordinates of another
+ candidate ORF, the longer one is reported. However, a single transcript can
+ report multiple ORFs (allowing for operons, chimeras, etc).
+ .
+ optional the putative peptide has a match to a Pfam domain above the noise
+ cutoff score.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9f2b0af
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: TransDecoder
+Source: https://github.com/TransDecoder/TransDecoder/archive/2.0.1.tar.gz
+Files-Excluded: transdecoder_plugins
+
+Files: *
+Copyright: (c) 2012, The Broad Institute, Inc. All rights reserved.
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: © 2015, Michigan State University
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+ .
+ · Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+ .
+ · Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+ .
+ · Neither the name of the Broad Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.**
+ .
+ THIS SOFTWARE IS PROVIDED BY THE BROAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BROAD INSTITUTE
+ BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..febcd91
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" <programname> > $MANDIR/<programname>.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..850d07a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,23 @@
+#!/usr/bin/make -f
+
+DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables you can
+# include /usr/share/cdbs/1/rules/buildvars.mk
+# and use what is set there. Any hint whether dh might set variables in
+# a similar manner are welcome.
+
+%:
+ dh $@
+
+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..d8b5812
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author:
+ Title:
+ Journal:
+ Year:
+ Volume:
+ Number:
+ Pages:
+ DOI:
+ PMID:
+ URL:
+ eprint:
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..a38a126
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+version=3
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
+ https://github.com/TransDecoder/Transdecoder/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
--
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