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 <[email protected]> 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 <[email protected]> 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.
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