debian/changelog

 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/compat

-9
+11

debian/control

@@ -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

 *.py			usr/share/qcumber
-config.txt	etc/qcumber
-parameter.txt	etc/qcumber
+config/adapters.fa	etc/qcumber
+config/config.txt	etc/qcumber
+config/parameter.txt	etc/qcumber
 *.tex			usr/share/qcumber
-*.R		usr/share/qcumber
+Rscripts		usr/share/qcumber
 *.html			usr/share/qcumber
 debian/bin		usr
-lib		usr/share/qcumber
\ No newline at end of file
+modules			usr/share/qcumber

debian/links

-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@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@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:
+ 
+ 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:
- 				from Bio import SeqIO
- 				seq_record = SeqIO.parse(arguments["reference"], "fasta")
+ 			seq_record = open(arguments["reference"], "r").readline()
+ 			assert seq_record.startswith(">"), "Reference file is not valid."

debian/patches/series

-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

 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@