add debian packaging

diff --git a/debian/README.source b/debian/README.source
new file mode 100644 (file)
index 0000000..98856d8
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,10 @@
+rsem for Debian
+---------------
+
+<this file describes information about the source package, see Debian policy
+manual section 4.14. You WILL either need to modify or delete this file>
+
+
+
+ -- Don Armstrong <don@debian.org>  Mon, 29 Sep 2014 11:06:49 -0700
+

diff --git a/debian/changelog b/debian/changelog
new file mode 100644 (file)
index 0000000..ed9751a
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+rsem (1.2.17-1) unstable; urgency=low
+
+  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
+
+ -- Don Armstrong <don@debian.org>  Mon, 29 Sep 2014 11:06:49 -0700

diff --git a/debian/control b/debian/control
new file mode 100644 (file)
index 0000000..f23c251
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,17 @@
+Source: rsem
+Section: unknown
+Priority: optional
+Maintainer: Don Armstrong <don@debian.org>
+Build-Depends: debhelper (>= 9),
+ r-base, perl, g++, 
+Standards-Version: 3.9.5
+Homepage: http://deweylab.biostat.wisc.edu/rsem/
+Vcs-Git: git://git.donarmstrong.com/rsem.git
+Vcs-Browser: http://git.donarmstrong.com/rsem.git
+
+Package: rsem
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ bowtie, samtools
+Description: RNA-Seq by Expectation-Maximization
+ RNA-Seq sequence aligner

diff --git a/debian/copyright b/debian/copyright
new file mode 100644 (file)
index 0000000..5f0e0f0
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: rsem
+Source: <url://example.com>
+
+Files: *
+Copyright: <years> <put author's name and email here>
+           <years> <likewise for another author>
+License: <special license>
+ <Put the license of the package here indented by 1 space>
+ <This follows the format of Description: lines in control file>
+ .
+ <Including paragraphs>
+
+# If you want to use GPL v2 or later for the /debian/* files use 
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2014 Don Armstrong <don@debian.org>
+License: GPL-2+
+ This package 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 2 of the License, or
+ (at your option) any later version.
+ .
+ This package 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.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid to pick license terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.

diff --git a/debian/rules b/debian/rules
new file mode 100755 (executable)
index 0000000..cf6e99e
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,37 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+#DH_VERBOSE = 1
+
+# see EXAMPLES in dpkg-buildflags(1) and read /usr/share/dpkg/*
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND  = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+# main packaging script based on dh7 syntax
+%:
+       dh $@ 
+
+# debmake generated override targets
+# This is example for Cmake (See http://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+#      dh_auto_configure -- \
+#      -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
+override_dh_auto_install:
+       dh_auto_install
+       install -d debian/rsem/usr/bin
+       install -t debian/rsem/usr/bin rsem-* convert-sam-for-rsem extract-transcript-to*
+
+
+
+

diff --git a/debian/source/format b/debian/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)