[med-svn] [bitseq] 01/14: New package - bitseq. Initial packaging tested for build on Ubuntu Precise. No ITP raised yet.
Andreas Tille
tille at debian.org
Sat Dec 2 08:47:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bitseq.
commit 1f5e01acbc30b054d383e44567975c16fd573eda
Author: Tim Booth <tbooth at ceh.ac.uk>
Date: Sat Feb 23 20:43:01 2013 +0000
New package - bitseq. Initial packaging tested for build on Ubuntu Precise.
No ITP raised yet.
---
debian/changelog | 8 ++++++++
debian/compat | 1 +
debian/control | 22 ++++++++++++++++++++++
debian/copyright | 15 +++++++++++++++
debian/patches/link_against_system_samtools | 29 +++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 21 +++++++++++++++++++++
debian/source/format | 1 +
debian/watch | 2 ++
9 files changed, 100 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..0a04e73
--- /dev/null
+++ b/debian/changelog
@@ -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
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..a1d6d86
--- /dev/null
+++ b/debian/control
@@ -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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..0cb9737
--- /dev/null
+++ b/debian/copyright
@@ -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'.
+
diff --git a/debian/patches/link_against_system_samtools b/debian/patches/link_against_system_samtools
new file mode 100644
index 0000000..6a55aba
--- /dev/null
+++ b/debian/patches/link_against_system_samtools
@@ -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
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..a6ef3fe
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+link_against_system_samtools
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..bb965fd
--- /dev/null
+++ b/debian/rules
@@ -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 ';'
+
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/watch b/debian/watch
new file mode 100644
index 0000000..15155db
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://code.google.com/p/bitseq/downloads/list .*/files/BitSeq-([0-9.]+).tar.gz
--
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