Commit 09e0b28e authored by Steffen Möller's avatar Steffen Möller
Browse files

Presumed usable.

parent 77fd212e

debian/changelog

+1 −1
Original line number Diff line number Diff line 
bcbio (1.0.9-1) UNRELEASED; urgency=medium



  * Initial release (Closes: #nnnn)

  * Initial release (Closes: #903386)



 -- Steffen Moeller <moeller@debian.org>  Sun, 11 Feb 2018 18:40:28 +0100

debian/control

+56 −4
Original line number Diff line number Diff line
@@ -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

0 → 100644
+6 −0
Original line number Diff line number Diff line 
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

+17 −0
Original line number Diff line number Diff line
@@ -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

+18 −1
Original line number Diff line number Diff line
@@ -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