[med-svn] [lofreq] 02/03: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Dec 24 08:07:20 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository lofreq.
commit 576dd0d5ba0476678f4dc4182e23ef00cac2eb53
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Dec 24 00:04:41 2015 -0800
Initial packaging
---
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 49 ++++++++++++++++++++++++++++++++++++
debian/copyright | 38 ++++++++++++++++++++++++++++
debian/docs | 1 +
debian/patches/external-htslib.patch | 16 ++++++++++++
debian/patches/series | 1 +
debian/rules | 14 +++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++++
10 files changed, 138 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..0670e51
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+lofreq (2.1.2+ds-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #808895)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Wed, 23 Dec 2015 11:35:17 -0800
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..62e9ed2
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,49 @@
+Source: lofreq
+Section: science
+Priority: optional
+Maintainer: Debian-Med-Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders:
+ Afif Elghraoui <afif at ghraoui.name>,
+Build-Depends:
+ debhelper (>= 9),
+ dh-autoreconf,
+ python-all,
+ zlib1g-dev,
+ libhts-dev,
+Standards-Version: 3.9.6
+Homepage: http://csb5.github.io/lofreq/
+Vcs-Git: git://anonscm.debian.org/debian-med/lofreq.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/lofreq.git
+
+Package: lofreq
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends}
+Description: sensitive variant calling from sequencing data
+ LoFreq* (i.e. LoFreq version 2) is a fast and sensitive
+ variant-caller for inferring SNVs and indels from next-generation
+ sequencing data. It makes full use of base-call qualities and other
+ sources of errors inherent in sequencing (e.g. mapping or base/indel
+ alignment uncertainty), which are usually ignored by other methods or
+ only used for filtering.
+ .
+ LoFreq* can run on almost any type of aligned sequencing data
+ (e.g. Illumina, IonTorrent or Pacbio) since no machine- or
+ sequencing-technology dependent thresholds are used. It automatically
+ adapts to changes in coverage and sequencing quality and can
+ therefore be applied to a variety of data-sets e.g.
+ viral/quasispecies, bacterial, metagenomics or somatic data.
+ .
+ LoFreq* is very sensitive; most notably, it is able to predict
+ variants below the average base-call quality (i.e. sequencing error
+ rate). Each variant call is assigned a p-value which allows for
+ rigorous false positive control. Even though it uses no
+ approximations or heuristics, it is very efficient due to several
+ runtime optimizations and also provides a (pseudo-)parallel
+ implementation. LoFreq* is generic and fast enough to be applied to
+ high-coverage data and large genomes. On a single processor it takes
+ a minute to analyze Dengue genome sequencing data with nearly 4000X
+ coverage, roughly one hour to call SNVs on a 600X coverage E.coli
+ genome and also roughly an hour to run on a 100X coverage human exome
+ dataset.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8b11120
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: lofreq
+Upstream-Contact: <wilma at gis.a-star.edu.sg>
+Source: https://github.com/CSB5/lofreq
+Files-Excluded:
+ dist/*
+ src/uthash/*
+
+Files: *
+Copyright: 2013-2014 Genome Institute of Singapore
+License: MIT
+
+Files: src/cdflib90/*
+Copyright: TODO
+License: TODO
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ 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 AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF 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/docs b/debian/docs
new file mode 100644
index 0000000..b43bf86
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README.md
diff --git a/debian/patches/external-htslib.patch b/debian/patches/external-htslib.patch
new file mode 100644
index 0000000..88542e7
--- /dev/null
+++ b/debian/patches/external-htslib.patch
@@ -0,0 +1,16 @@
+Description: Allow linking to external htslib
+ The build system looks for the static library in the
+ same directory as the headers, which is not the case
+ for the externally installed version. In fact, we should
+ probably try to avoid static linking to htslib.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-12-24
+--- lofreq.orig/src/lofreq/Makefile.am
++++ lofreq/src/lofreq/Makefile.am
+@@ -29,4 +29,4 @@
+
+ # note: order matters
+ #lofreq_LDADD = @htslib_dir@/libhts.a @samtools_dir@/libbam.a
+-lofreq_LDADD = @HTSLIB@/libhts.a @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
++lofreq_LDADD = -L at HTSLIB@ -lhts @SAMTOOLS@/libbam.a ../cdflib90/libcdf.a
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..45de3dd
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+external-htslib.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..9dd9841
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+#include /usr/share/dpkg/default.mk
+
+export HTSLIB=/usr/include
+# samtools does not package its header files...
+# We'll also need its libbam.a file, which isn't provided by the
+# samtools package the way we have it currently.
+#
+#export SAMTOOLS=/usr/lib/python2.7/dist-packages/pysam/include/samtools
+
+%:
+ dh $@ --parallel --with autoreconf
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..4896823
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ Author: Andreas Wilm and Pauline Poh Kim Aw and Denis Bertrand and Grace Hui Ting Yeo and Swee Hoe Ong and Chang Hua Wong and Chiea Chuen Khor and Rosemary Petric and Martin Lloyd Hibberd and Niranjan Nagarajan
+ Title: "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets"
+ Journal: Nucleic Acids Research
+ Year: 2012
+ Volume: 40
+ Number: 22
+ Pages: 11189-11201
+ DOI: 10.1093/nar/gks918
+ PMID: 23066108
+ URL: http://nar.oxfordjournals.org/content/40/22/11189.abstract
+ eprint: http://nar.oxfordjournals.org/content/40/22/11189.full.pdf+html
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