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 <[email protected]> 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 <[email protected]> +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 <[email protected]> + +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
