[med-svn] [Git][med-team/qcumber][master] 8 commits: Fix again watch file
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 27 07:15:22 BST 2018
Andreas Tille pushed to branch master at Debian Med / qcumber
Commits:
e322eebe by Andreas Tille at 2018-09-17T12:38:19Z
Fix again watch file
- - - - -
dac4f4ef by Andreas Tille at 2018-09-17T12:42:31Z
use pybuild
- - - - -
303201bb by Andreas Tille at 2018-09-17T12:59:39Z
Adapt patches
- - - - -
df99ba91 by Andreas Tille at 2018-09-17T13:01:00Z
Remove ancient X-Python-Version field
- - - - -
33fa980f by Andreas Tille at 2018-09-17T13:01:35Z
debhelper 11
- - - - -
0ade3bce by Andreas Tille at 2018-09-17T13:02:50Z
Point Vcs fields to salsa.debian.org
- - - - -
f680efb2 by Andreas Tille at 2018-09-17T13:02:50Z
Standards-Version: 4.2.1
- - - - -
f3a64956 by Andreas Tille at 2018-09-17T14:48:51Z
Depends: snakemake, fix installation
- - - - -
10 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/install
- debian/links
- debian/patches/adapt_config.patch
- debian/patches/check_fasta.patch
- debian/patches/series
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,18 @@
qcumber (2.0.3+dfsg-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* New usptream version
* Fix watch file
+ * Remove ancient X-Python-Version field
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Depends: snakemake
[ Steffen Moeller ]
* Created debian/upstream/metadata - yet no entries in catalogs.
- -- Andreas Tille <tille at debian.org> Mon, 21 Aug 2017 14:41:51 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 17 Sep 2018 15:02:51 +0200
qcumber (1.0.14+dfsg-1) unstable; urgency=medium
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
@@ -3,19 +3,19 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
dh-python,
python3-all,
+ python3-setuptools,
fastqc,
trimmomatic,
bowtie2,
kraken,
texlive-latex-base
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/qcumber.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/qcumber.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/qcumber
+Vcs-Git: https://salsa.debian.org/med-team/qcumber.git
Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber
-X-Python-Version: >= 3.4
Package: qcumber
Architecture: all
@@ -31,7 +31,8 @@ Depends: ${python3:Depends},
r-base-core,
r-bioc-savr,
r-cran-ggplot2,
- r-cran-quantreg
+ r-cran-quantreg,
+ snakemake
Conflicts: qc-pipeline
Provides: qc-pipeline
Replaces: qc-pipeline
=====================================
debian/install
=====================================
@@ -1,8 +1,9 @@
-*.py usr/share/qcumber
-config.txt etc/qcumber
-parameter.txt etc/qcumber
-*.tex usr/share/qcumber
-*.R usr/share/qcumber
-*.html usr/share/qcumber
-debian/bin usr
-lib usr/share/qcumber
\ No newline at end of file
+*.py usr/share/qcumber
+config/adapters.fa etc/qcumber
+config/config.txt etc/qcumber
+config/parameter.txt etc/qcumber
+*.tex usr/share/qcumber
+Rscripts usr/share/qcumber
+*.html usr/share/qcumber
+debian/bin usr
+modules usr/share/qcumber
=====================================
debian/links
=====================================
@@ -1,5 +1,4 @@
-etc/qcumber/parameter.txt usr/share/qcumber/parameter.txt
-etc/qcumber/config.txt usr/share/qcumber/config.txt
+etc/qcumber usr/share/qcumber/config
usr/share/javascript/angular.js/angular.min.js usr/share/qcumber/lib/angular.min.js
usr/share/javascript/bootstrap/css/bootstrap-theme.min.css usr/share/qcumber/lib/bootstrap-theme.min.css
usr/share/javascript/bootstrap/css/bootstrap.min.css usr/share/qcumber/lib/bootstrap.min.css
=====================================
debian/patches/adapt_config.patch
=====================================
@@ -2,20 +2,12 @@ Author: Andreas Tille <TilleA at rki.de>
Last-Update: Wed, 16 Mar 2016 11:01:55 +0100
Description: Use Debian packaged locations
---- a/config.txt
-+++ b/config.txt
-@@ -1,10 +1,10 @@
+--- a/config/config.txt
++++ b/config/config.txt
+@@ -1,4 +1,4 @@
[DEFAULT]
--kraken_db = /opt/common/pipelines/databases/minikraken_20141208/
+-kraken_db =
+-adapter = $CONDA_PREFIX/share/trimmomatic/adapters
+kraken_db = /var/lib/kraken/minikraken_20141208
-
- [PATH]
- kraken =
--adapter = /opt/common/pipelines/tools/Trimmomatic-0.36/adapters/
--fastqc = /opt/common/pipelines/tools/FastQC_0.11.5/
--trimmomatic = /opt/common/pipelines/tools/Trimmomatic-0.36/
+adapter = /usr/share/trimmomatic/
-+fastqc =
-+trimmomatic = /usr/bin
- bowtie2 =
=====================================
debian/patches/check_fasta.patch
=====================================
@@ -2,11 +2,11 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 14 Mar 2017 12:40:48 +0100
Description: Check properly formated reference file
---- a/QCumber.py
-+++ b/QCumber.py
-@@ -32,6 +32,24 @@ global r2_pattern
- global sep_pattern
- global lane_pattern
+--- a/QCumber-2
++++ b/QCumber-2
+@@ -201,11 +201,28 @@ def get_input():
+
+ return type, sample_dict, join_lanes, name_dict, join_reads
+from sys import stderr
+from Bio import SeqIO
@@ -25,18 +25,13 @@ Description: Check properly formated reference file
+ except:
+ print('%s %s does not contain valid fasta data' % (filetype, fastafile), file=stderr)
+ return False
-+
- def get_illumina_reads(tmp):
- readsets = []
- if not all([re.search(lane_pattern, x) for x in arguments["r1"]]):
-@@ -255,8 +273,8 @@ def check_input_validity():
- if not arguments["reference"]:
- sys.exit("Mapping needs a reference.")
- else:
-- if not os.path.exists(arguments["reference"]):
-- sys.exit("Reference does not exist.")
-+ if not check_fasta(arguments["reference"],"Reference"):
-+ sys.exit(1)
- try:
- from Bio import SeqIO
- seq_record = SeqIO.parse(arguments["reference"], "fasta")
+
+ def check_input_validity():
+ if arguments["reference"]:
+- if not os.path.exists(arguments["reference"]):
+- sys.exit("Reference does not exist.")
++ if not check_fasta(arguments["reference"],"Reference"):
++ sys.exit(1)
+ try:
+ seq_record = open(arguments["reference"], "r").readline()
+ assert seq_record.startswith(">"), "Reference file is not valid."
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,3 @@
-set_absolute_path_to_tex_template.patch
+# set_absolute_path_to_tex_template.patch
adapt_config.patch
check_fasta.patch
=====================================
debian/rules
=====================================
@@ -3,7 +3,7 @@
# DH_VERBOSE := 1
%:
- dh $@ --with python3 # --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
override_dh_compress:
dh_compress --exclude=.pdf
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s/@ANY_VERSION@\/.*\.tar\.gz/QCumber-$1\.tar\.gz/g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://gitlab.com/RKIBioinformaticsPipelines/QCumber/tags?sort=updated_desc .*/repository/@ANY_VERSION@/archive\.tar\.gz
+ https://gitlab.com/RKIBioinformaticsPipelines/QCumber/tags?sort=updated_desc .*/archive/.*/QCumber at ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/qcumber/compare/b8c4125012a211d8f92f837afdac49fe0577acca...f3a64956765d768a15d816289a8baf062f4f428d
--
View it on GitLab: https://salsa.debian.org/med-team/qcumber/compare/b8c4125012a211d8f92f837afdac49fe0577acca...f3a64956765d768a15d816289a8baf062f4f428d
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