[med-svn] [ea-utils] 02/03: Rather maintain package in Git since the upstream tarball was changed
Andreas Tille
tille at debian.org
Sat Jul 25 06:14:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ea-utils.
commit 5ac1c9ce685f319d4c03d7e22a300d7c43c7d1f1
Author: Andreas Tille <tille at debian.org>
Date: Sat Jul 25 08:12:20 2015 +0200
Rather maintain package in Git since the upstream tarball was changed
---
debian/changelog | 22 ++++++++++++++++++++++
debian/compat | 1 +
debian/control | 44 +++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 25 ++++++++++++++++++++++++
debian/createmanpages | 16 ++++++++++++++++
debian/patches/makefile_patch | 26 +++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 31 ++++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 ++++++++++++
debian/watch | 3 +++
11 files changed, 182 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7016687
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,22 @@
+ea-utils (1.1.2+dfsg-1) UNRELEASED; urgency=medium
+
+ * Initial upload to Debian (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Sat, 25 Jul 2015 07:51:46 +0200
+
+ea-utils (1.1.2-0biolinux4) trusty; urgency=medium
+
+ * Re-remove utility copy of sparsehash as v2 is now in the
+ PPA.
+ * And don't forget to re-add the dependency
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 22 Jan 2015 18:30:36 +0000
+
+ea-utils (1.1.2-0biolinux2) trusty; urgency=low
+
+ * Initial release for Bio-Linux 8
+ * Build against samtools from Debian.
+ * Leave utility copy of sparsehash in for now, as Trusty
+ has v1 of the lib and we want v2.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 19 Aug 2014 16:19:00 +0100
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..9dd2a89
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,44 @@
+Source: ea-utils
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libbam-dev,
+ zlib1g-dev,
+ libgsl0-dev,
+ libsparsehash-dev (>= 2.0)
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
+Homepage: https://code.google.com/p/ea-utils/
+
+Package: ea-utils
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ r-base-core
+Description: Command-line tools for processing biological sequencing data
+ ...barcode demultiplexing, adapter trimming, etc.
+ .
+ Primarily written to support an Illumina based pipeline - but should work with
+ any FASTQs.
+ .
+ Main Tools are:
+ .
+ * fastq-mcf
+ Scans a sequence file for adapters, and, based on a log-scaled threshold,
+ determines a set of clipping parameters and performs clipping. Also does
+ skewing detection and quality filtering.
+ * fastq-multx
+ Demultiplexes a fastq. Capable of auto-determining barcode id's based on a
+ master set fields. Keeps multiple reads in-sync during demultiplexing. Can
+ verify that the reads are in-sync as well, and fail if they're not.
+ * fastq-join
+ Similar to audy's stitch program, but in C, more efficient and supports some
+ automatic benchmarking and tuning. It uses the same "squared distance for
+ anchored alignment" as other tools.
+ * varcall
+ Takes a pileup and calculates variants in a more easily parameterized manner
+ than some other tools.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fc6aa30
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,25 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ea-utils
+Source: https://code.google.com/p/ea-utils/source/checkout
+Files-Excluded: google
+ samtools
+ sparsehash
+
+Files: *
+Copyright: © 2011 Erik Aronesty <erik at q32.com>
+ 2003-2006 Heng Li <lh3lh3 at live.co.uk>
+ 2008 Jue Ruan <ruanjue at gmail.com>
+ Gunjan Hariani,
+ 2008-2009 Genome Research Ltd.,
+ 2010 Illumina, Inc
+License: MIT
+
+Files: debian/*
+Copyright: © 2014 Tim Booth <tbooth at ceh.ac.uk>
+ © 2015 Andreas Tille <tille at debian.org>
+License: MIT
+
+TODO:
+ - use debian packaged samtools
+ - use debian packaged sparsehash
+ - some remaining files have BSD-3-clause
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..febcd91
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" <programname> > $MANDIR/<programname>.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
diff --git a/debian/patches/makefile_patch b/debian/patches/makefile_patch
new file mode 100644
index 0000000..abce167
--- /dev/null
+++ b/debian/patches/makefile_patch
@@ -0,0 +1,26 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Tue, 19 Aug 2014 16:19:00 +0100
+Description: Adapt Makefile to use Debian packaged libraries
+
+--- a/Makefile
++++ b/Makefile
+@@ -77,12 +77,8 @@
+ $(CC) $(CFLAGS) gcModel.c -o $@ $<
+
+ # why the libbam.a doesn't work? not sure... *.o works
+-sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h
+-ifeq ($(OS),Windows_NT)
+- $(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
+-else
+- $(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@
+-endif
++sam-stats: sam-stats.cpp fastq-lib.h
++ $(CC) $(CFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@
+
+ samtools/libbam.a: samtools/*.c samtools/*.h
+ cd samtools && make libbam.a
+@@ -102,4 +98,3 @@
+
+ clean:
+ rm -f *.o $(BIN)
+- cd samtools && make clean
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..6a0d9f3
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+makefile_patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..88913a2
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,31 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# To build with packages sparsehash change this to -I/usr/include/google
+export CFLAGS:=$(CFLAGS) -I/usr/include/google
+export CPPFLAGS:=$(CPPFLAGS) -I/usr/include/google
+
+%:
+ dh $@
+
+override_dh_auto_install:
+ dh_auto_install -- PREFIX='$${DESTDIR}/usr'
+
+override_dh_auto_clean:
+ dh_auto_clean
+
+override_dh_clean:
+ dh_clean
+ #Kill convenience copies of code
+ rm -rf samtools
+ rm -rf google sparsehash
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..29dda79
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Cite-As:
+ Erik Aronesty (2011). ea-utils : "Command-line tools for processing biological sequencing data"; http://code.google.com/p/ea-utils
+Reference:
+ Author: Erik Aronesty
+ Title: Comparison of Sequencing Utility Programs
+ Journal: The Open Bioinformatics Journal
+ Year: 2013
+ Volume: 7
+ Pages: 1-8
+ DOI: 10.2174/1875036201307010001
+ URL: http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1
+ eprint: http://benthamopen.com/contents/pdf/TOBIOIJ/TOBIOIJ-7-1.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..e20aa30
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+# Upstream was linked via Google Drive, so there is no hope of a working watchfile.
--
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