[med-svn] [Git][med-team/rosa][master] Added rosa package, fixed lintian warning

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / rosa


Commits:
a3aa3f68 by Steffen Möller at 2020-07-04T12:32:10+02:00
Added rosa package, fixed lintian warning

- - - - -


2 changed files:

- debian/control
- debian/rules


Changes:

=====================================
debian/control
=====================================
@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),
                python3-setuptools,
                python3-all,
                r-cran-lsd
+#   sambamba <!nocheck>
 Standards-Version: 4.5.0
 Homepage: https://github.com/bartongroup/RoSA
 Vcs-Browser: https://salsa.debian.org/med-team/rosa
@@ -16,6 +17,41 @@ Vcs-Git: https://salsa.debian.org/med-team/rosa.git
 Testsuite: autopkgtest-pkg-python
 Rules-Requires-Root: no
 
+Package: rosa
+Architecture: all
+Depends: r-other-rosa,
+         python3-rosa,
+         ${misc:Depends},
+Description: Removal of Spurious Antisense in biological RNA sequences
+ In stranded RNA-Seq experiments it is possible to detect and
+ measure antisense transcription, important since antisense transcripts
+ impact gene transcription in several different ways. Stranded RNA-Seq
+ determines the strand from which an RNA fragment originates, and so can
+ be used to identify where antisense transcription may be implicated in
+ gene regulation.
+ .
+ However, spurious antisense reads are often present in experiments, and
+ can manifest at levels greater than 1% of sense transcript levels. This
+ is enough to disrupt analyses by causing false antisense counts to
+ dominate the set of genes with high antisense transcription levels.
+ .
+ The RoSA (Removal of Spurious Antisense) tool detects the presence of
+ high levels of spurious antisense transcripts, by:
+  * analysing ERCC spike-in data to find the ratio of antisense:sense
+    transcripts in the spike-ins; or
+  * using antisense and sense counts around splice sites to provide a
+    set of gene-specific estimates; or
+  * both.
+ .
+ Once RoSA has an estimate of the spurious antisense, expressed as a
+ ratio of antisense:sense counts, RoSA will calculate a correction to
+ the antisense counts based on the ratio. Where a gene-specific estimate
+ is available for a gene, it will be used in preference to the global
+ estimate obtained from either spike-ins or spliced reads.
+ .
+ This package provides the library for the statistics suite R.
+
+
 Package: r-other-rosa
 Architecture: all
 Section: gnu-r
@@ -55,8 +91,9 @@ Package: python3-rosa
 Architecture: all
 Section: python
 Depends: ${python3:Depends},
-         ${misc:Depends}
-Recommends: rosa
+         ${misc:Depends},
+Recommends: r-other-rosa,
+            sambamba
 Description: Removal of Spurious Antisense in biological RNA sequences (Python3)
  In stranded RNA-Seq experiments it is possible to detect and
  measure antisense transcription, important since antisense transcripts


=====================================
debian/rules
=====================================
@@ -18,12 +18,12 @@ override_dh_auto_install:
 	dh_auto_install -O--buildsystem=R --sourcedirectory=$(CURDIR)
 	mv debian/tmp tmp-install
 	dh_auto_install --sourcedirectory=python --buildsystem=pybuild
-	#cd python && ( [ -r debian ] || ln -s ../debian . ) && pybuild --install
+	find debian/python3-rosa -name *.csv | xargs -r chmod -x
 
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -rf debian/rosa debian/tmp/ debian/python3-rosa
-	rm -rf python/.pybuild rm -rf python/rosa.egg-info
+	rm -rf python/.pybuild rm -rf python/rosa.egg-info python/rosa/__pycache__ python/rosa/tests/__pycache__ python/.pytest_cache .pybuild tmp-install
 	rm  -f python/debian
 
 # FIXME: override_dh_auto_test:



View it on GitLab: https://salsa.debian.org/med-team/rosa/-/commit/a3aa3f6815adfcab85bee65c14f4b29dcfc3d9a5

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View it on GitLab: https://salsa.debian.org/med-team/rosa/-/commit/a3aa3f6815adfcab85bee65c14f4b29dcfc3d9a5
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