[med-svn] [Git][med-team/bcbio][master] Added documentation.

[Steffen Möller]

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

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/ac76425d9f89be07c4584863a22eedc077f63b29
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