This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository qcumber.
commit 6e3bebdec8c543d2944e590ff90f1cd2b666c382 Author: Andreas Tille <[email protected]> Date: Wed Feb 15 08:55:53 2017 +0100 Adapt patches --- debian/control | 1 - debian/patches/adapt_config.patch | 30 ++++++++++---------- debian/patches/config_in_etc.patch | 33 ---------------------- debian/patches/python3_explicit.patch | 12 -------- debian/patches/series | 2 -- .../set_absolute_path_to_tex_template.patch | 32 ++++++++++----------- debian/patches/use_smaller_try-except_blocks.patch | 23 --------------- debian/rules | 2 +- 8 files changed, 32 insertions(+), 103 deletions(-) diff --git a/debian/control b/debian/control index 6c96917..e91e6d5 100644 --- a/debian/control +++ b/debian/control @@ -10,7 +10,6 @@ Build-Depends: debhelper (>= 9), trimmomatic, bowtie2, kraken, - dos2unix, texlive-latex-base Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/qcumber.git diff --git a/debian/patches/adapt_config.patch b/debian/patches/adapt_config.patch index 2ed3767..80da0a6 100644 --- a/debian/patches/adapt_config.patch +++ b/debian/patches/adapt_config.patch @@ -5,18 +5,18 @@ Description: Use Debian packaged locations --- a/config.txt +++ b/config.txt @@ -1,10 +1,10 @@ - [DEFAULT] --kraken_db =/home/andruscha/software/kraken/minikraken_20141208/ -+kraken_db =/var/lib/kraken/minikraken_20141208 - - [PATH] --kraken = --adapter = /data/GS/tools/Trimmomatic-0.32/adapters/ --fastqc = /home/lieuv/tools/FastQC/ --trimmomatic = -+kraken = /usr/lib/kraken -+adapter = /usr/share/trimmomatic/ -+fastqc = -+trimmomatic = /usr/bin/ - bowtie2 = - + [DEFAULT] +-kraken_db =/opt/common/pipelines/databases/minikraken_20141208/ ++kraken_db =/var/lib/kraken/minikraken_20141208 + + [PATH] +-kraken = +-adapter = /data/GS/tools/Trimmomatic-0.32/adapters/ +-fastqc = /opt/common/pipelines/tools/FastQC_0.11.5/ +-trimmomatic = ++kraken = /usr/lib/kraken ++adapter = /usr/share/trimmomatic/ ++fastqc = ++trimmomatic = /usr/bin + bowtie2 = + diff --git a/debian/patches/config_in_etc.patch b/debian/patches/config_in_etc.patch deleted file mode 100644 index 26a2370..0000000 --- a/debian/patches/config_in_etc.patch +++ /dev/null @@ -1,33 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 16 Mar 2016 11:01:55 +0100 -Description: Config file should be in /etc/qcumber - This patch is deyctivated and it is done via symlinks since all - attempts to get this working failed so far. - ---- a/classes.py -+++ b/classes.py -@@ -13,11 +13,11 @@ from collections import OrderedDict - import base64 - - default_parameter = configparser.ConfigParser() --default_parameter.read(join(dirname(__file__), "parameter.txt")) -+default_parameter.read(join("/etc/qcumber", "parameter.txt")) - - def get_tool_path(name, section="PATH"): - config = configparser.ConfigParser() -- config.read(join(dirname(__file__), "config.txt")) -+ config.read(join("/etc/qcumber", "config.txt")) - path_dict = config[section] - return path_dict[name] - ---- a/QCumber.py -+++ b/QCumber.py -@@ -22,7 +22,7 @@ except ImportError: - - - parameter = configparser.ConfigParser() --parameter.read(join(dirname(__file__), "parameter.txt")) -+parameter.read(join(dirname(__file__), "/etc/qcumber/parameter.txt")) - - file_extensions = parameter["Fileextension"]["fastq"] - r1_pattern = parameter["Pattern"]["R1"] diff --git a/debian/patches/python3_explicit.patch b/debian/patches/python3_explicit.patch deleted file mode 100644 index 05d51bb..0000000 --- a/debian/patches/python3_explicit.patch +++ /dev/null @@ -1,12 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 16 Mar 2016 11:01:55 +0100 -Description: seems dh-python needs proper first line - ---- a/QCumber.py -+++ b/QCumber.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python3 -+#!/usr/bin/python3 - # -*- coding: utf-8 -*- - __author__ = 'LieuV' - __version__ = "1.0.1" diff --git a/debian/patches/series b/debian/patches/series index c9b5dc5..56c9d55 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,2 @@ -python3_explicit.patch set_absolute_path_to_tex_template.patch adapt_config.patch -use_smaller_try-except_blocks.patch diff --git a/debian/patches/set_absolute_path_to_tex_template.patch b/debian/patches/set_absolute_path_to_tex_template.patch index 1ad0932..67d53a0 100644 --- a/debian/patches/set_absolute_path_to_tex_template.patch +++ b/debian/patches/set_absolute_path_to_tex_template.patch @@ -5,19 +5,19 @@ Description: Inside the Debian package we know exactly the location of the --- a/QCumber.py +++ b/QCumber.py -@@ -162,10 +162,11 @@ def writeReport(sample, arguments): - report_name = os.path.join(sample.mainResultsPath, "Report", - "summary_" + sample.name + "_" + datetime.datetime.strftime(datetime.datetime.now(), "%d-%m-%y_%H-%M")) - print("Writing latex " ,report_name) -- env = Environment() -- env.loader = FileSystemLoader(os.path.dirname(__file__)) -- -- template = env.get_template("report.tex") -+ template_dir = '/usr/share/qcumber' -+ template_file = 'report.tex' -+ loader = FileSystemLoader(template_dir) -+ env = Environment(loader=loader) -+ template = env.get_template(template_file) - pdf_latex = template.render(sample=sample, pipeline=Pipeline(), trim_param = sample.readSets[0].trimRes.print_param(arguments["palindrome"],arguments["minlen"], arguments["trimOption"])) - - latex = open(report_name + ".tex", "w") +@@ -168,10 +168,11 @@ def writeReport(sample, arguments): + report_name = os.path.join(sample.mainResultsPath, "Report", + "summary_" + sample.name + "_" + datetime.datetime.strftime(datetime.datetime.now(), "%d-%m-%y_%H-%M")) + print("Writing latex " ,report_name) +- env = Environment() +- env.loader = FileSystemLoader(os.path.dirname(__file__)) +- +- template = env.get_template("report.tex") ++ template_dir = '/usr/share/qcumber' ++ template_file = 'report.tex' ++ loader = FileSystemLoader(template_dir) ++ env = Environment(loader=loader) ++ template = env.get_template(template_file) + pdf_latex = template.render(sample=sample, pipeline=Pipeline(), trim_param = sample.readSets[0].trimRes.print_param(arguments["palindrome"],arguments["minlen"], arguments["trimOption"])) + + latex = open(report_name + ".tex", "w") diff --git a/debian/patches/use_smaller_try-except_blocks.patch b/debian/patches/use_smaller_try-except_blocks.patch deleted file mode 100644 index af54904..0000000 --- a/debian/patches/use_smaller_try-except_blocks.patch +++ /dev/null @@ -1,23 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 16 Mar 2016 11:01:55 +0100 -Description: use smaller try-except blocks - ---- a/QCumber.py -+++ b/QCumber.py -@@ -437,10 +437,16 @@ def main(arguments): - for line in iter(process.stderr.readline, b''): - print(line) - process.communicate() -+ except: -+ print("Creating boxplot result in", join(arguments["output"],"QCResults", "Report", "src", plot["file"]), "failed") -+ try: - #plot barplots - tmp_overview.close() - process = subprocess.Popen(" ".join(["Rscript --vanilla ", join(os.path.dirname(__file__), "barplot.R"),join(tmp, "overview.csv"), - join(arguments["output"], "QCResults/Report/src/img")]),stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) -+ except: -+ print("Rscript --vanilla ", join(os.path.dirname(__file__), "barplot.R"), "overview.csv failed") -+ try: - for line in iter(process.stderr.readline, b''): - print(line) - process.communicate() diff --git a/debian/rules b/debian/rules index ffb0af5..f312997 100755 --- a/debian/rules +++ b/debian/rules @@ -17,7 +17,7 @@ override_dh_fixperms: chmod a-x debian/*/usr/share/*/helper.py chmod a-x debian/*/usr/share/*/barplot.R chmod a-x debian/*/usr/share/*/*.html - dos2unix debian/*/usr/share/*/*.py +# dos2unix debian/*/usr/share/*/*.py #dos2unix debian/*/etc/qcumber/*.txt #get-orig-source: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qcumber.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
