[med-svn] [qcumber] 05/07: Adapt patches
Andreas Tille
tille at debian.org
Wed Feb 15 09:48:53 UTC 2017
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 <tille at debian.org>
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 <TilleA at rki.de>
-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 <TilleA at rki.de>
-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 <TilleA at rki.de>
-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:
--
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