[med-svn] r13077 - in trunk/packages: . bitseq bitseq/trunk bitseq/trunk/debian bitseq/trunk/debian/patches bitseq/trunk/debian/source mgltools/scenario/trunk

Timothy Booth tbooth-guest at alioth.debian.org
Sat Feb 23 20:43:02 UTC 2013 

Author: tbooth-guest
Date: 2013-02-23 20:43:01 +0000 (Sat, 23 Feb 2013)
New Revision: 13077

Added:
   trunk/packages/bitseq/
   trunk/packages/bitseq/trunk/
   trunk/packages/bitseq/trunk/debian/
   trunk/packages/bitseq/trunk/debian/changelog
   trunk/packages/bitseq/trunk/debian/compat
   trunk/packages/bitseq/trunk/debian/control
   trunk/packages/bitseq/trunk/debian/copyright
   trunk/packages/bitseq/trunk/debian/patches/
   trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools
   trunk/packages/bitseq/trunk/debian/patches/series
   trunk/packages/bitseq/trunk/debian/rules
   trunk/packages/bitseq/trunk/debian/source/
   trunk/packages/bitseq/trunk/debian/source/format
   trunk/packages/bitseq/trunk/debian/watch
   trunk/packages/mgltools/scenario/trunk/debian/
Log:
New package - bitseq.  Initial packaging tested for build on Ubuntu Precise.
No ITP raised yet.


Added: trunk/packages/bitseq/trunk/debian/changelog
===================================================================
--- trunk/packages/bitseq/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/changelog	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,8 @@
+bitseq (0.4.3-0ubuntu2) precise; urgency=low
+
+  * Initial release.
+  * Build against stock libbam (only static just now)
+  * Build against stock libboost
+  * For now, leave the names of the binaries as-is
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Mon, 11 Feb 2013 09:59:05 +0000

Added: trunk/packages/bitseq/trunk/debian/compat
===================================================================
--- trunk/packages/bitseq/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/compat	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1 @@
+9

Added: trunk/packages/bitseq/trunk/debian/control
===================================================================
--- trunk/packages/bitseq/trunk/debian/control	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/control	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,22 @@
+Source: bitseq
+Section: science
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 9), zlib1g-dev, libbam-dev, libboost1.48-dev
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/bitseq/
+
+Package: bitseq
+Architecture: any
+Pre-Depends: dpkg (>= 1.15.6~)
+Depends: ${shlibs:Depends}, ${misc:Depends}, python-minimal
+Suggests: samtools
+Description: Bayesian Inference of Transcripts from Sequencing Data
+ BitSeq is an application for inferring expression levels of individual
+ transcripts from sequencing (RNA-Seq) data and estimating differential
+ expression (DE) between conditions. An advantage of this approach is the
+ ability to account for both technical uncertainty and intrinsic biological
+ variance in order to avoid false DE calls. The technical contribution to the
+ uncertainty comes both from finite read-depth and the possibly ambiguous
+ mapping of reads to multiple transcripts.

Added: trunk/packages/bitseq/trunk/debian/copyright
===================================================================
--- trunk/packages/bitseq/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/copyright	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,15 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BitSeq
+Upstream-Contact: Peter Glaus <glaus at cs.man.ac.uk>
+
+Files: *
+Copyright: © 2013 Peter Glaus
+License: Artistic 2
+
+License: Artistic 2
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic'.
+

Added: trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools
===================================================================
--- trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/patches/link_against_system_samtools	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,29 @@
+--- a/ReadDistribution.h
++++ b/ReadDistribution.h
+@@ -21,8 +21,8 @@
+ 
+ #else
+ 
+-#include "bam.h"
+-#include "sam.h"
++#include <samtools/bam.h>
++#include <samtools/sam.h>
+ 
+ //#define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
+ /*
+--- a/Makefile
++++ b/Makefile
+@@ -25,11 +25,8 @@
+ getWithinGeneExpression: getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o common.h
+ 	$(CXX) $(CXXFLAGS) getWithinGeneExpression.cpp common.o ArgumentParser.o TranscriptInfo.o PosteriorSamples.o -o getWithinGeneExpression
+ 
+-parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o samtools/sam.o
+-	$(CXX) $(CXXFLAGS) $(OPENMP) -Isamtools samtools/*.o common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lz -o parseAlignment
+-
+-samtools/sam.o:
+-	make --directory samtools
++parseAlignment: parseAlignment.cpp common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o
++	$(CXX) $(CXXFLAGS) $(OPENMP) common.o ArgumentParser.o TranscriptInfo.o TranscriptSequence.o TranscriptExpression.o ReadDistribution.o parseAlignment.cpp -lbam -lz -o parseAlignment
+ 
+ convertSamples: convertSamples.cpp common.o ArgumentParser.o TranscriptInfo.o
+ 	$(CXX) $(CXXFLAGS) convertSamples.cpp common.o ArgumentParser.o  TranscriptInfo.o -o convertSamples

Added: trunk/packages/bitseq/trunk/debian/patches/series
===================================================================
--- trunk/packages/bitseq/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/patches/series	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1 @@
+link_against_system_samtools

Added: trunk/packages/bitseq/trunk/debian/rules
===================================================================
--- trunk/packages/bitseq/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/rules	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,21 @@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
+
+%:
+	dh $@
+
+override_dh_builddeb:
+	dh_builddeb -- -Z xz
+
+override_dh_clean:
+	dh_clean
+	rm -rf boost samtools
+
+override_dh_auto_clean:
+	dh_auto_clean || true
+
+override_dh_auto_install:
+	find -maxdepth 1 -type f -perm /111 -exec dh_install '{}' /usr/bin ';'
+


Property changes on: trunk/packages/bitseq/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/bitseq/trunk/debian/source/format
===================================================================
--- trunk/packages/bitseq/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/source/format	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/bitseq/trunk/debian/watch
===================================================================
--- trunk/packages/bitseq/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/bitseq/trunk/debian/watch	2013-02-23 20:43:01 UTC (rev 13077)
@@ -0,0 +1,2 @@
+version=3
+http://code.google.com/p/bitseq/downloads/list .*/files/BitSeq-([0-9.]+).tar.gz

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