[med-svn] [Git][med-team/bcbio][master] Fine-tuning for first upload

Steffen Möller gitlab at salsa.debian.org
Mon Jan 21 21:39:27 GMT 2019 

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
ab7dd934 by Steffen Möller at 2019-01-21T21:38:49Z
Fine-tuning for first upload

- - - - -


7 changed files:

- + debian/README.Debian
- + debian/bcbio.lintian-overrides
- debian/changelog
- debian/control
- − debian/manpages
- − debian/python3-bcbio.lintian-overrides
- debian/rules


Changes:

=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,8 @@
+bcbio-nextgen
+=============
+
+This package builds and tests fine, but the documentation is not yet packaged.
+
+Please be aware of related Debian packages for toil and cwltool.
+
+ -- Steffen Moeller   Mon, 21 Jan 2019 21:30:11 +0100


=====================================
debian/bcbio.lintian-overrides
=====================================
@@ -0,0 +1,8 @@
+# Better not mess with the community that expects these binaries
+# just like they are.
+bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py
+bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py
+bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py
+bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py
+bcbio: script-with-language-extension usr/bin/cwltool2wdl.py
+


=====================================
debian/changelog
=====================================
@@ -2,4 +2,6 @@ bcbio (1.1.2-1) unstable; urgency=medium
 
   * Initial release (Closes: #903386)
 
+    TODO: Documentation not built
+
  -- Steffen Moeller <moeller at debian.org>  Thu, 17 Jan 2019 16:37:37 +0100


=====================================
debian/control
=====================================
@@ -16,9 +16,12 @@ Build-Depends: debhelper (>= 10),
                python3-pyvcf,
                python3-toolz,
                python3-tornado,
+               python3-yaml,
 # for testing
+               python3-biopython,
                python3-cyvcf2,
-               python3-logbook
+               python3-logbook,
+               python3-requests
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/bcbio
 Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
@@ -29,10 +32,8 @@ Architecture: all
 Depends: ${python3:Depends},
          ${misc:Depends},
          python3-seqcluster,
-         python3-tornado,
-         python3-yaml
-Suggests: toil
-Description: toolkit for analysing high-throughput sequencing data
+         python3-tornado
+Description: library 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.
@@ -43,3 +44,21 @@ 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: bcbio
+Architecture: all
+Depends: ${python3:Depends},
+         ${misc:Depends},
+         python3-bcbio
+Suggests: toil, cwltool
+Description: toolkit for analysing high-throughput sequencing data
+ This package installs the command line tools 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.


=====================================
debian/manpages deleted
=====================================
@@ -1,6 +0,0 @@
-debian/bcbio_fastq_umi_prep.py.1
-debian/bcbio_nextgen.py.1
-debian/bcbio_nextgen_install.py.1
-debian/bcbio_prepare_samples.py.1
-debian/bcbio_setup_genome.py.1
-debian/cwltool2wdl.py.1


=====================================
debian/python3-bcbio.lintian-overrides deleted
=====================================
@@ -1,8 +0,0 @@
-# Better not mess with the community that expects these binaries
-# just like they are.
-python3-bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py
-python3-bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py
-python3-bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py
-python3-bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py
-python3-bcbio: script-with-language-extension usr/bin/cwltool2wdl.py
-


=====================================
debian/rules
=====================================
@@ -10,20 +10,27 @@ export PYBUILD_NAME=bcbio
 #override_dh_auto_test:
 #	echo "No testing."
 
-override_dh_auto_install: manpages
+override_dh_auto_install:
 	dh_auto_install
-	#[ -d debian/python-bcbio-bin ] && mkdir -p debian/python-bcbio-bin/usr/bin
-	#mkdir -p debian/python3-bcbio-bin/usr/bin
-	#[ -d debian/python-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 
+	[ -d debian/bcbio ] && mkdir -p debian/bcbio/usr/bin
+	mv debian/python3-bcbio/usr/bin/* debian/bcbio/usr/bin/
+	# To keep awareness of redundant binaries with different versions of Python
+	#mkdir -p debian/bcbio/usr/bin
 	#rm -rf debian/python-bcbio/usr/bin debian/python3-bcbio/usr/bin
 	
+# Problem with a series of tools that need bcbio before it is installed,
+# just to print --help
 
 manpages: debian/bcbio_nextgen.1
 debian/bcbio_nextgen.1: scripts/bcbio_nextgen.py
+	mkdir -p debian/bcbio/usr/share/man/man1
+	export PYTHONPATH=debian/usr/lib/python3/dist-packages ; \
 	for py in scripts/*.py; do \
-	  help2man --no-discard-stderr -h $$py python > debian/$$(basename $$py).1 ; \
+	  help2man -N -s 1 --no-discard-stderr -h $$py -n $$(basename $$py .py) python | gzip -c > debian/bcbio/usr/share/man/man1/$$(basename $$py).1.gz ; \
 	done
+	# problem with --help generation
+	find debian -name bcbio_fastq_umi_prep.py.1* -delete
+	find debian -name bcbio_prepare_samples.py.1* -delete
 
 override_dh_auto_clean:
 	dh_auto_clean



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd
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/20190121/fe368cb2/attachment-0001.html>

More information about the debian-med-commit mailing list