[med-svn] [Git][med-team/lumpy-sv][master] 2 commits: Adapt pathes to Debian locations
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 1 19:55:12 BST 2020
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 <tille at debian.org> 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 <tille at debian.org>
+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 $LUMPY_DIR/lumpyexpress.config file\n"
++ echo -e "Error: neither samtools nor sambamba were found. Please set path of one of these in /etc/lumpy-sv/lumpyexpress.config file\n"
+ exit 1
+ fi
+
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
use_debian_packaged_libs.patch
+lumpyexpress.config.patch
=====================================
debian/patches/use_debian_packaged_libs.patch
=====================================
@@ -1,3 +1,10 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 26 May 2020 15:07:58 +0200
+Description: Use Debian packaged libraries
+ Please note: lumpy-sv contains a code copy of bedtools. Unfortunately
+ bedtools does not have a development library so its hard to replace this
+ code copy here.
+
--- a/Makefile
+++ b/Makefile
@@ -24,21 +24,18 @@ endif
=====================================
debian/rules
=====================================
@@ -25,3 +25,11 @@ include /usr/share/dpkg/default.mk
#ifeq (,$(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
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