[med-svn] [Git][med-team/bcbio][master] Added documentation.
Steffen Möller
gitlab at salsa.debian.org
Wed Jan 23 20:19:30 GMT 2019
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 <moeller at debian.org> 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 <moeller at debian.org> 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
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