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 <[email protected]> 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.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
