Steffen Möller pushed to branch master at Debian Med / bcbio
Commits: ac76425d by Steffen Möller at 2019-01-23T20:17:43Z Added documentation. - - - - - 8 changed files: - + debian/bcbio-doc.dirs - + debian/bcbio-doc.doc-base - + debian/bcbio-doc.docs - + debian/bcbio-doc.lintian-overrides - + debian/bcbio.manpages - debian/changelog - debian/control - debian/rules Changes: ===================================== debian/bcbio-doc.dirs ===================================== @@ -0,0 +1 @@ +usr/share/doc/bcbio-doc ===================================== debian/bcbio-doc.doc-base ===================================== @@ -0,0 +1,11 @@ +Document: bcbio +Title: Debian BCBio-NextGen Manual +Author: Brad Chapman +Abstract: The document describes all aspects + of workflows supported by BCBio and the + technology underneath. +Section: Science/Medicine + +Format: HTML +Index: /usr/share/doc/bcbio-doc/html/index.html +Files: /usr/share/doc/bcbio-doc/html/*.html ===================================== debian/bcbio-doc.docs ===================================== @@ -0,0 +1 @@ +build/html/ ===================================== debian/bcbio-doc.lintian-overrides ===================================== @@ -0,0 +1,3 @@ +# Yes. This should eventually be transformed into a local link. +bcbio-doc: privacy-breach-generic usr/share/doc/bcbio-doc/html/contents/cwl.html [<img alt="variant calling overview" src="http://i.imgur.com/iyu8viz.png"; style="width: 600px; height: 700px;" />] (http://i.imgur.com/iyu8viz.png) + ===================================== debian/bcbio.manpages ===================================== @@ -0,0 +1 @@ +build/man/bcbio_nextgen.1 ===================================== debian/changelog ===================================== @@ -1,10 +1,17 @@ -bcbio (1.1.2-2) unstable; urgency=medium +bcbio (1.1.2-3) unstable; urgency=medium + + * Demoted python3-seqcluster to become a recommendation + * Packaged documentation, which also contributed a man page + + -- Steffen Moeller <[email protected]> Wed, 23 Jan 2019 15:04:57 +0100 + +bcbio (1.1.2-2) UNRELEASED; urgency=medium * Found Python3 incompatbility. Upstream has it already. -- Steffen Moeller <[email protected]> Mon, 21 Jan 2019 23:56:26 +0100 -bcbio (1.1.2-1) unstable; urgency=medium +bcbio (1.1.2-1) UNRELEASED; urgency=medium * Initial release (Closes: #903386) ===================================== debian/control ===================================== @@ -21,7 +21,9 @@ Build-Depends: debhelper (>= 10), python3-biopython, python3-cyvcf2, python3-logbook, - python3-requests + python3-requests, +# documentation + python3-sphinx Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/bcbio Vcs-Git: https://salsa.debian.org/med-team/bcbio.git @@ -33,6 +35,7 @@ Depends: ${python3:Depends}, ${misc:Depends}, python3-tornado Recommends: python3-seqcluster +Suggests: bcbio-doc 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 @@ -50,7 +53,8 @@ Architecture: all Depends: ${python3:Depends}, ${misc:Depends}, python3-bcbio -Suggests: toil, cwltool +Suggests: toil, cwltool, + bcbio-doc 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 @@ -62,3 +66,18 @@ 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-doc +Architecture: all +Depends: ${sphinxdoc:Depends},${misc:Depends}, +Suggests: bcbio|python3-bcbio +Description: Documentation for RNAseq-workflows of bcbio(-nextgen) + This package provides the documentation for all aspects of the + workflows and technology of the bcbio-nextgen toolkit. + . + 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/rules ===================================== @@ -4,11 +4,12 @@ export DH_VERBOSE = 1 export PYBUILD_NAME=bcbio %: - dh $@ --with python3 --buildsystem=pybuild + dh $@ --with python3,sphinxdoc --buildsystem=pybuild - -#override_dh_auto_test: -# echo "No testing." +override_dh_auto_build: + dh_auto_build + PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml docs build/html # HTML generator + PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bman docs build/man # Manpage generator override_dh_auto_install: dh_auto_install View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ac76425d9f89be07c4584863a22eedc077f63b29 -- View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ac76425d9f89be07c4584863a22eedc077f63b29 You're receiving this email because of your account on salsa.debian.org.
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