[med-svn] [Git][med-team/lumpy-sv][master] 4 commits: Add own config file
Andreas Tille
gitlab at salsa.debian.org
Mon Jun 1 20:42:32 BST 2020
Andreas Tille pushed to branch master at Debian Med / lumpy-sv
Commits:
bc88ad19 by Andreas Tille at 2020-06-01T21:10:02+02:00
Add own config file
- - - - -
ce521e21 by Andreas Tille at 2020-06-01T21:22:01+02:00
Better description
- - - - -
186dabe6 by Andreas Tille at 2020-06-01T21:22:31+02:00
Spelling
- - - - -
2971fffc by Andreas Tille at 2020-06-01T21:42:12+02:00
Add python3 to Build-Depends
- - - - -
6 changed files:
- debian/control
- debian/copyright
- + debian/etc/lumpyexpress.config
- debian/install
- debian/patches/lumpyexpress.config.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -4,6 +4,8 @@ Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
+ dh-python,
+ python3,
libbamtools-dev,
libfastahack-dev,
libgzstream-dev,
@@ -20,6 +22,7 @@ Package: lumpy-sv
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
+ ${python3:Depends},
samblaster,
samtools,
python3,
@@ -28,8 +31,6 @@ Depends: ${shlibs:Depends},
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
- improved sensitivity, especially when SV signal is reduced owing to
- either low coverage data or low intra-sample variant allele frequency.
- We also report a set of 4,564 validated breakpoints from the NA12878
- human genome.
+ SV signals jointly across multiple samples. LUMPY yields improved
+ sensitivity, especially when SV signal is reduced owing to either low
+ coverage data or low intra-sample variant allele frequency.
=====================================
debian/copyright
=====================================
@@ -12,20 +12,20 @@ Copyright: 2011-2014 Ryan M. Layer
License: MIT
Files:
- */utils/BamTools-Ancillary
- */utils/BlockedIntervals
- */utils/Point
- */utils/VectorOps
- */utils/bedFile
- */utils/bedFilePE
- */utils/bedGraphFile
- */utils/chromsweep
- */utils/fileType
- */utils/genomeFile
- */utils/lineFileUtilities
- */utils/sequenceUtilities
- */utils/stringUtilities
- */utils/tabFile
+ src/utils/BamTools-Ancillary/*
+ src/utils/BlockedIntervals/*
+ src/utils/Point/*
+ src/utils/VectorOps/*
+ src/utils/bedFile/*
+ src/utils/bedFilePE/*
+ src/utils/bedGraphFile/*
+ src/utils/chromsweep/*
+ src/utils/fileType/*
+ src/utils/genomeFile/*
+ src/utils/lineFileUtilities/*
+ src/utils/sequenceUtilities/*
+ src/utils/stringUtilities/*
+ src/utils/tabFile/*
Copyright: 2009-2011 Aaron Quinlan
2010 - Assaf Gordon, CSHL
License: GPL-2
=====================================
debian/etc/lumpyexpress.config
=====================================
@@ -0,0 +1,13 @@
+LUMPY_HOME=/usr/share/lumpy-sv
+
+LUMPY=/usr/bin/lumpy
+HEXDUMP=/usr/bin/hexdump
+SAMBLASTER=/usr/bin/samblaster
+SAMBAMBA=/usr/bin/sambamba
+SAMTOOLS=/usr/bin/samtools
+PYTHON=/usr/bin/python3
+
+PAIREND_DISTRO=/usr/share/lumpy-sv/scripts/pairend_distro.py
+#BAMGROUPREADS=/usr/share/lumpy-sv/scripts/bamkit/bamgroupreads.py
+#BAMFILTERRG=/usr/share/lumpy-sv/scripts/bamkit/bamfilterrg.py
+#BAMLIBS=/usr/share/lumpy-sv/scripts/bamkit/bamlibs.py
=====================================
debian/install
=====================================
@@ -1,5 +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/etc/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
=====================================
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 26 May 2020 15:07:58 +0200
-Description: Adapt pathes to Debian locations
+Description: Adapt paths to Debian locations
--- a/scripts/lumpyexpress
+++ b/scripts/lumpyexpress
=====================================
debian/rules
=====================================
@@ -4,21 +4,11 @@
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-# specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@
+ dh $@ --with python3
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
@@ -33,3 +23,6 @@ override_dh_install:
override_dh_link:
dh_link
dh_link /etc/$(DEB_SOURCE)/lumpyexpress.config /usr/share/$(DEB_SOURCE)/scripts/lumpyexpress.config
+
+override_dh_python3:
+ dh_python3 --shebang=/usr/bin/python3
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb
--
View it on GitLab: https://salsa.debian.org/med-team/lumpy-sv/-/compare/f42ed0e5e81dd0f7c49a33dc3e2dedf1fbba819d...2971fffc423487daf71caf3f94337c702d4996fb
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200601/c9588037/attachment-0001.html>
More information about the debian-med-commit
mailing list