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debian/changelog
View file @ f3a64956
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@debian.org> Mon, 21 Aug 2017 14:41:51 +0200
-- Andreas Tille <tille@debian.org> Mon, 17 Sep 2018 15:02:51 +0200
qcumber (1.0.14+dfsg-1) unstable; urgency=medium
......
debian/control
View file @ f3a64956
......@@ -3,19 +3,19 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@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
View file @ f3a64956
*.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
View file @ f3a64956
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
View file @ f3a64956
......@@ -2,20 +2,12 @@ Author: Andreas Tille <TilleA@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
View file @ f3a64956
......@@ -2,11 +2,11 @@ Author: Andreas Tille <tille@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
View file @ f3a64956
set_absolute_path_to_tex_template.patch
# set_absolute_path_to_tex_template.patch
adapt_config.patch
check_fasta.patch
debian/rules
View file @ f3a64956
......@@ -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
View file @ f3a64956
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@ANY_VERSION@@ARCHIVE_EXT@