[med-svn] r19705 - in trunk/packages: . ea-utils ea-utils/trunk ea-utils/trunk/debian ea-utils/trunk/debian/patches ea-utils/trunk/debian/source ea-utils/trunk/debian/upstream

Sat Jul 25 05:43:00 UTC 2015

Author: tille
Date: 2015-07-25 05:42:59 +0000 (Sat, 25 Jul 2015)
New Revision: 19705

Added:
   trunk/packages/ea-utils/
   trunk/packages/ea-utils/trunk/
   trunk/packages/ea-utils/trunk/debian/
   trunk/packages/ea-utils/trunk/debian/changelog
   trunk/packages/ea-utils/trunk/debian/compat
   trunk/packages/ea-utils/trunk/debian/control
   trunk/packages/ea-utils/trunk/debian/copyright
   trunk/packages/ea-utils/trunk/debian/createmanpages
   trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git
   trunk/packages/ea-utils/trunk/debian/patches/
   trunk/packages/ea-utils/trunk/debian/patches/makefile_patch
   trunk/packages/ea-utils/trunk/debian/patches/series
   trunk/packages/ea-utils/trunk/debian/rules
   trunk/packages/ea-utils/trunk/debian/source/
   trunk/packages/ea-utils/trunk/debian/source/format
   trunk/packages/ea-utils/trunk/debian/upstream/
   trunk/packages/ea-utils/trunk/debian/upstream/metadata
   trunk/packages/ea-utils/trunk/debian/watch
Log:
Inject further dependency of qiime as packaged by BioLinux


Added: trunk/packages/ea-utils/trunk/debian/changelog
===================================================================

--- trunk/packages/ea-utils/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/changelog	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,16 @@
+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

Added: trunk/packages/ea-utils/trunk/debian/compat
===================================================================
--- trunk/packages/ea-utils/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/compat	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1 @@
+9

Added: trunk/packages/ea-utils/trunk/debian/control
===================================================================
--- trunk/packages/ea-utils/trunk/debian/control	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/control	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,38 @@
+Source: ea-utils
+Section: science
+Priority: optional
+Maintainer: Tim Booth <tbooth at ceh.ac.uk>
+Uploaders: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Build-Depends: debhelper (>= 9), libbam-dev, zlib1g-dev, libgsl0-dev,
+               libsparsehash-dev (>= 2.0)
+Standards-Version: 3.9.5
+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.

Added: trunk/packages/ea-utils/trunk/debian/copyright
===================================================================
--- trunk/packages/ea-utils/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/copyright	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,16 @@
+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: *
+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>
+License: MIT

Added: trunk/packages/ea-utils/trunk/debian/createmanpages
===================================================================
--- trunk/packages/ea-utils/trunk/debian/createmanpages	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/createmanpages	2015-07-25 05:42:59 UTC (rev 19705)
@@ -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
+


Property changes on: trunk/packages/ea-utils/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git
===================================================================
--- trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+
+echo "Please verify whether this script is obsoleted by gbp-create-remote-repo !"
+
+# This script implements the "Git tips" given here
+#   http://debian-med.alioth.debian.org/docs/policy.html#git-tips
+# Use it with caution since it is less testet
+
+DEBPKGNAME=`dpkg-parsechangelog | awk '/^Source:/ {print $2}'`
+SHORTDESC=`grep "^Description: " debian/control | head -n 1 | sed 's/^Description: //'`
+VCSGIT=`grep "^Vcs-Git: " debian/control | sed -e 's/^Vcs-Git: //' -e 's#git://anonscm.debian.org/#ssh://git.debian.org/git/#'`
+DIRatALIOTH=`echo $VCSGIT | sed -e 's#ssh://git.debian.org/git/#/git/#' -e 's#/[^/]\+\.git##'`
+
+ssh git.debian.org "cd $DIRatALIOTH; ./setup-repository $DEBPKGNAME '$SHORTDESC'"
+git remote add origin $VCSGIT
+git push origin master
+git push --all --set-upstream
+git push --tags


Property changes on: trunk/packages/ea-utils/trunk/debian/inject-into-alioth-git
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/ea-utils/trunk/debian/patches/makefile_patch
===================================================================
--- trunk/packages/ea-utils/trunk/debian/patches/makefile_patch	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/patches/makefile_patch	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,22 @@
+--- 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

Added: trunk/packages/ea-utils/trunk/debian/patches/series
===================================================================
--- trunk/packages/ea-utils/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/patches/series	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1 @@
+makefile_patch

Added: trunk/packages/ea-utils/trunk/debian/rules
===================================================================
--- trunk/packages/ea-utils/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/rules	2015-07-25 05:42:59 UTC (rev 19705)
@@ -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=-I.
+export CPPFLAGS=-I.
+
+%:
+	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


Property changes on: trunk/packages/ea-utils/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/ea-utils/trunk/debian/source/format
===================================================================
--- trunk/packages/ea-utils/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/source/format	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/ea-utils/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/ea-utils/trunk/debian/upstream/metadata	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/upstream/metadata	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,12 @@
+Reference:
+  Author: Erik Aronesty
+  Title: Comparison of Sequencing Utility Programs
+  Journal: The Open Bioinformatics Journal
+  Year:2013
+  Volume:
+  Number:
+  Pages:8
+  DOI: 10.2174/1875036201307010001
+  PMID:
+  URL: http://benthamopen.com/openaccess.php?tobioij/articles/V007/1TOBIOIJ.htm
+  eprint:

Added: trunk/packages/ea-utils/trunk/debian/watch
===================================================================
--- trunk/packages/ea-utils/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/ea-utils/trunk/debian/watch	2015-07-25 05:42:59 UTC (rev 19705)
@@ -0,0 +1,3 @@
+version=3
+
+# Upstream was linked via Google Drive, so there is no hope of a working watchfile.


