[med-svn] [Git][med-team/bcbio][master] Presumed usable.
Steffen Möller
gitlab at salsa.debian.org
Tue Jul 10 11:44:57 BST 2018
Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
09e0b28e by Steffen Möller at 2018-07-10T12:44:20+02:00
Presumed usable.
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/manpages
- debian/patches/python3_transition.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
bcbio (1.0.9-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #nnnn)
+ * Initial release (Closes: #903386)
-- Steffen Moeller <moeller at debian.org> Sun, 11 Feb 2018 18:40:28 +0100
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 10),
python3-logbook,
python-pysam,
python3-pysam,
-# python3-pybedtools,
+ python3-pybedtools,
python3-gffutils,
python-cyvcf2,
python3-cyvcf2,
@@ -24,7 +24,11 @@ Build-Depends: debhelper (>= 10),
python-pandas,
python3-pandas,
python-mock,
- python3-mock
+ python3-mock,
+ python-seqcluster,
+ python3-seqcluster,
+ python-tornado,
+ python3-tornado
Standards-Version: 4.1.5
Vcs-Browser: https://salsa.debian.org/med-team/bcbio
Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
@@ -33,7 +37,9 @@ Homepage: https://github.com/chapmanb/bcbio-nextgen
Package: python-bcbio
Architecture: all
Depends: ${python:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python-seqcluster,
+ python-tornado
#Suggests: python-bcbio-doc
Description: toolkit for analysing high-throughput sequencing data
This package installs the Python 2 libraries of the bcbio-nextgen
@@ -50,7 +56,9 @@ Description: toolkit for analysing high-throughput sequencing data
Package: python3-bcbio
Architecture: all
Depends: ${python3:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python3-seqcluster,
+ python3-tornado
#Suggests: python-bcbio-doc
Description: toolkit for analysing high-throughput sequencing data
This package installs the Python 3 libraries of the bcbio-nextgen
@@ -63,3 +71,47 @@ Description: toolkit for analysing high-throughput sequencing data
contributes a shared community resource that handles the data processing
component of sequencing analysis, providing researchers with more time
to focus on the downstream biology.
+
+Package: python-bcbio-bin
+Architecture: all
+Depends: ${python3:Depends},
+ ${misc:Depends},
+ python-seqcluster,
+ python-tornado
+Conflicts: python3-bcbio-bin
+#Suggests: python-bcbio-doc
+Description: toolkit for analysing high-throughput sequencing data
+ This package installs the Python 3 libraries of the bcbio-nextgen
+ toolkit implementing best-practice pipelines for fully automated high
+ throughput sequencing analysis.
+ .
+ A high-level configuration file specifies inputs and analysis parameters
+ to drive a parallel pipeline that handles distributed execution,
+ idempotent processing restarts and safe transactional steps. The project
+ contributes a shared community resource that handles the data processing
+ component of sequencing analysis, providing researchers with more time
+ to focus on the downstream biology.
+ .
+ This package offers the Python2-based command line interface to bcbio.
+
+Package: python3-bcbio-bin
+Architecture: all
+Depends: ${python3:Depends},
+ ${misc:Depends},
+ python3-seqcluster,
+ python3-tornado
+Conflicts: python-bcbio-bin
+#Suggests: python-bcbio-doc
+Description: toolkit for analysing high-throughput sequencing data
+ This package installs the Python 3 libraries of the bcbio-nextgen
+ toolkit implementing best-practice pipelines for fully automated high
+ throughput sequencing analysis.
+ .
+ A high-level configuration file specifies inputs and analysis parameters
+ to drive a parallel pipeline that handles distributed execution,
+ idempotent processing restarts and safe transactional steps. The project
+ contributes a shared community resource that handles the data processing
+ component of sequencing analysis, providing researchers with more time
+ to focus on the downstream biology.
+ .
+ This package offers the Python3-based command line interface to bcbio.
=====================================
debian/manpages
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1,6 @@
+debian/bcbio_fastq_umi_prep.1
+debian/bcbio_nextgen.1
+debian/bcbio_nextgen_install.1
+debian/bcbio_prepare_samples.1
+debian/bcbio_setup_genome.1
+debian/cwltool2wdl.1
=====================================
debian/patches/python3_transition.patch
=====================================
--- a/debian/patches/python3_transition.patch
+++ b/debian/patches/python3_transition.patch
@@ -11,3 +11,20 @@ Index: bcbio/tests/integration/test_pipeline.py
class TestVCFUtil(object):
+Index: bcbio/scripts/bcbio_nextgen.py
+===================================================================
+--- bcbio.orig/scripts/bcbio_nextgen.py
++++ bcbio/scripts/bcbio_nextgen.py
+@@ -199,10 +199,10 @@ def _add_inputs_to_kwargs(args, kwargs,
+ elif len(inputs) == 3:
+ global_config, fc_dir, run_info_yaml = inputs
+ elif args.version:
+- print version.__version__
++ print(version.__version__)
+ sys.exit()
+ else:
+- print "Incorrect input arguments", inputs
++ print("Incorrect input arguments", inputs)
+ parser.print_help()
+ sys.exit()
+ if fc_dir:
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,7 @@ export DH_VERBOSE = 1
export PYBUILD_NAME=bcbio
%:
- dh $@ --with python2,python3 --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
# If you need to rebuild the Sphinx documentation
@@ -20,6 +20,23 @@ export PYBUILD_NAME=bcbio
override_dh_auto_test:
echo "No testing."
+override_dh_auto_install: manpages
+ dh_auto_install
+ mkdir -p debian/python-bcbio-bin/usr/bin debian/python3-bcbio-bin/usr/bin
+ mv debian/python-bcbio/usr/bin/* debian/python-bcbio-bin/usr/bin
+ mv debian/python3-bcbio/usr/bin/* debian/python3-bcbio-bin/usr/bin
+ rm -rf debian/python-bcbio/usr/bin debian/python3-bcbio/usr/bin
+
+
+manpages: debian/bcbio_nextgen.1
+debian/bcbio_nextgen.1: scripts/bcbio_nextgen.py
+ for py in scripts/*.py; do \
+ help2man --no-discard-stderr -h $$py python > debian/$$(basename $$py .py).1 ; \
+ done
+
override_dh_auto_clean:
dh_auto_clean
rm -f bcbio/pipeline/version.py
+ rm -f debian/*.1
+
+.PHONY: manpages
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/09e0b28ed48105785a9ae4b9bd7a7f86efbb2cb1
--
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/09e0b28ed48105785a9ae4b9bd7a7f86efbb2cb1
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/20180710/28d84563/attachment-0001.html>
More information about the debian-med-commit
mailing list