[med-svn] [SCM] cufflinks branch, master, updated. upstream/0.9.3-13-gad6acd0
Alex Mestiashvili
alex at biotec.tu-dresden.de
Thu May 5 08:44:58 UTC 2011
The following commit has been merged in the master branch:
commit ad6acd04bca4212804d9a8fb6ef5697509a008f8
Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
Date: Thu May 5 08:37:03 2011 +0000
new debian dir for cufflinks
diff --git a/debian/changelog b/debian/changelog
index 1752b71..68447dd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-cufflinks (0.9.3-1) UNRELEASED; urgency=low
+cufflinks (0.9.3-1) unstable; urgency=low
* Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
- -- Charles Plessy <plessy at debian.org> Sun, 30 Jan 2011 10:32:38 +0900
+ -- Alex Mestiashvili <alex at biotec.tu-dresden.de> Tue, 03 May 2011 13:53:19 +0000
diff --git a/debian/control b/debian/control
index a31cb0e..3b7554a 100644
--- a/debian/control
+++ b/debian/control
@@ -1,10 +1,11 @@
Source: cufflinks
Section: science
Priority: optional
-Maintainer: Charles Plessy <plessy at debian.org>
-Build-Depends: cdbs, debhelper (>= 7.0.50~), autotools-dev,
- libboost-dev (>= 1.40) | libboost1.40-dev
-Standards-Version: 3.9.0
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev , libboost-dev (>=1.38.0) , libbam-dev
+Standards-Version: 3.9.1
Homepage: http://cufflinks.cbcb.umd.edu/
Vcs-Git: git://git.debian.org/debian-med/cufflinks.git
Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
@@ -17,4 +18,4 @@ Description: Transcript assembly, differential expression, and differential regu
differential expression and regulation in RNA-Seq samples. It accepts aligned
RNA-Seq reads and assembles the alignments into a parsimonious set of
transcripts. Cufflinks then estimates the relative abundances of these
- transcripts based on how many reads support each one.
+ transcripts based on how many reads support each one.
diff --git a/debian/copyright b/debian/copyright
index 09f8991..a81072b 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,34 +1,41 @@
+Format : http://dep.debian.net/deps/dep5
+Upstream-Name : cufflinks
+Source : http://cufflinks.cbcb.umd.edu/downloads/
-NOTE THAT THERE IS MUCH MORE TO DOCUMENT.
+Files: *
+Copyright: <years> <put author's name and email here>
+ <years> <likewise for another author>
+License: BSL-1
-Name : Cufflinks
-Contact : Cole Trapnell <cole at cs.umd.edu>
-Source : http://cufflinks.cbcb.umd.edu/downloads/
+Files: debian/*
+Copyright: 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+License: GPL-3.0+
License : BSL-1
-
- ===========================================================================
- Boost Software License, Version 1.0
- ===========================================================================
-
- Permission is hereby granted, free of charge, to any person or organization
- obtaining a copy of the software and accompanying documentation covered by
- this license (the "Software") to use, reproduce, display, distribute,
- execute, and transmit the Software, and to prepare derivative works of the
- Software, and to permit third-parties to whom the Software is furnished to
- do so, all subject to the following:
-
- The copyright notices in the Software and this entire statement, including
- the above license grant, this restriction and the following disclaimer,
- must be included in all copies of the Software, in whole or in part, and
- all derivative works of the Software, unless such copies or derivative
- works are solely in the form of machine-executable object code generated by
- a source language processor.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
- SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
- FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
- ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS IN THE SOFTWARE.
+
+ ===========================================================================
+ Boost Software License, Version 1.0
+ ===========================================================================
+
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
+
diff --git a/debian/patches/configure.patch b/debian/patches/configure.patch
new file mode 100644
index 0000000..b8d86ff
--- /dev/null
+++ b/debian/patches/configure.patch
@@ -0,0 +1,11 @@
+--- cufflinks-0.9.3.orig/configure
++++ cufflinks-0.9.3/configure
+@@ -4014,7 +4014,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
+
+- #include <bam/bam.h>
++ #include <bam.h>
+
+ int
+ main ()
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
new file mode 100644
index 0000000..4063d3a
--- /dev/null
+++ b/debian/patches/fix_includes_path.patch
@@ -0,0 +1,11 @@
+--- cufflinks-0.9.3.orig/src/hits.h
++++ cufflinks-0.9.3/src/hits.h
+@@ -16,7 +16,7 @@
+
+ #include <boost/shared_ptr.hpp>
+
+-#include <bam/sam.h>
++#include <sam.h>
+
+ #include "common.h"
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..207657b
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+configure.patch
+fix_includes_path.patch
diff --git a/debian/rules b/debian/rules
index 5b92f85..20fa0b4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,5 +1,7 @@
#!/usr/bin/make -f
+# -*- makefile -*-
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/autotools.mk
-#include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+%:
+ dh $@
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)
--
Transcript assembly, differential expression, and differential regulation for RNA-Seq.
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