Andreas Tille pushed to branch master at Debian Med / lumpy-sv
Commits: baa6c087 by Andreas Tille at 2020-06-01T20:54:22+02:00 Adapt pathes to Debian locations - - - - - f42ed0e5 by Andreas Tille at 2020-06-01T20:54:48+02:00 Install files - - - - - 7 changed files: - debian/changelog - debian/control - + debian/install - + debian/patches/lumpyexpress.config.patch - debian/patches/series - debian/patches/use_debian_packaged_libs.patch - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -2,13 +2,5 @@ lumpy-sv (0.3.0+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) TODO: https://github.com/hall-lab/bamkit - - TODO2: argh, bedtools code copy is linked here - so the removal does not really work - src/lumpy/SV_Bedpe.cpp:#include "BamAncillary.h" - src/lumpy/SV_SplitRead.cpp:#include "BamAncillary.h" - src/lumpy/lumpy.cpp:#include "BamAncillary.h" - src/lumpy/bp_softclip_fa.cpp:#include "BamAncillary.h" - src/lumpy/SV_Pair.cpp:#include "BamAncillary.h" - -- Andreas Tille <[email protected]> Tue, 26 May 2020 15:07:58 +0200 ===================================== debian/control ===================================== @@ -19,7 +19,13 @@ Homepage: https://github.com/arq5x/lumpy-sv Package: lumpy-sv Architecture: any Depends: ${shlibs:Depends}, - ${misc:Depends} + ${misc:Depends}, + samblaster, + samtools, + python3, + python3-pysam, + python3-numpy +Recommends: sambamba Description: general probabilistic framework for structural variant discovery LUMPY, a novel SV discovery framework that naturally integrates multiple SV signals jointly across multiple samples. We show that LUMPY yields ===================================== debian/install ===================================== @@ -0,0 +1,5 @@ +bin/lumpyexpress.config etc/lumpy +scripts usr/share/lumpy-sv +bin/lumpy usr/bin +bin/lumpy_filter usr/bin +bin/lumpyexpress usr/bin ===================================== debian/patches/lumpyexpress.config.patch ===================================== @@ -0,0 +1,62 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 26 May 2020 15:07:58 +0200 +Description: Adapt pathes to Debian locations + +--- a/scripts/lumpyexpress ++++ b/scripts/lumpyexpress +@@ -62,14 +62,14 @@ source_binaries() { + else + echo "Config file $1 not found. Attempting to auto-source executables" + # general +- LUMPY_HOME=$( dirname `which lumpyexpress` ) ++ LUMPY_HOME=/usr/share/lumpy-sv + + LUMPY=`which lumpy || true` + SAMBLASTER=`which samblaster || true` + SAMBAMBA=`which sambamba || true` + SAMTOOLS=`which samtools || true` + # python 2.7 or newer, must have pysam, numpy installed +- PYTHON=`which python || true` ++ PYTHON=`which python3 || true` + + # For testing if the full BAM is actually a CRAM! + HEXDUMP=`which hexdump || true` +@@ -126,7 +126,7 @@ options: + + # set defaults + LUMPY_DIR=`dirname $0` +-CONFIG="$LUMPY_DIR/lumpyexpress.config" ++CONFIG="/etc/lumpy-sv/lumpyexpress.config" + THREADS=1 + ANNOTATE=0 + MIN_SAMPLE_WEIGHT=4 +@@ -228,17 +228,17 @@ source_binaries $CONFIG + if [[ -z "$LUMPY" ]] + then + usage +- echo -e "Error: lumpy executable not found. Please set path in $LUMPY_DIR/lumpyexpress.config file\n" ++ echo -e "Error: lumpy executable not found. Please set path in /etc/lumpy-sv/lumpyexpress.config file\n" + exit 1 + elif [[ -z "$PAIREND_DISTRO" ]] + then + usage +- echo -e "Error: pairend_distro.py executable not found. Please set path in $LUMPY_DIR/lumpyexpress.config file\n" ++ echo -e "Error: pairend_distro.py executable not found. Please set path in /etc/lumpy-sv/lumpyexpress.config file\n" + exit 1 + elif [[ -z "$BAMFILTERRG" ]] + then + usage +- echo -e "Error: bamfilterrg.py executable not found. Please set path in $LUMPY_DIR/lumpyexpress.config file\n" ++ echo -e "Error: bamfilterrg.py executable not found. Please set path in /etc/lumpy-sv/lumpyexpress.config file\n" + exit 1 + fi + +@@ -259,7 +259,7 @@ then + SAMSORT="$SAMTOOLS sort -m 1G -T " + else + usage +- echo -e "Error: neither samtools nor sambamba were found. Please set path of one of these in $LUMPY_DIR/lumpyexpress.config file\n" ++ echo -e "Error: neither samtools nor sambamba were found. Please set path of one of these in /etc/lumpy-sv/lumpyexpress.config file\n" + exit 1 + fi + ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ use_debian_packaged_libs.patch +lumpyexpress.config.patch ===================================== debian/patches/use_debian_packaged_libs.patch ===================================== @@ -1,3 +1,10 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 26 May 2020 15:07:58 +0200 +Description: Use Debian packaged libraries + Please note: lumpy-sv contains a code copy of bedtools. Unfortunately + bedtools does not have a development library so its hard to replace this + code copy here. + --- a/Makefile +++ b/Makefile @@ -24,21 +24,18 @@ endif ===================================== debian/rules ===================================== @@ -25,3 +25,11 @@ include /usr/share/dpkg/default.mk #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) # do_stuff_for_testing #endif + +override_dh_install: + dh_install + rm debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config + +override_dh_link: + dh_link + dh_link /etc/$(DEB_SOURCE)/lumpyexpress.config /usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/068b269665be20e3d69b163ec2b663eae3a60662...f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d -- View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/068b269665be20e3d69b163ec2b663eae3a60662...f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d You're receiving this email because of your account on salsa.debian.org.
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