[med-svn] [qcumber] 02/02: Adapt patches to new upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 2f2d41d488eddc1a490d32203db64954feb203a8
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 23 09:43:59 2016 +0100

    Adapt patches to new upstream version
---
 debian/patches/adapt_config.patch                    | 15 ++++++++-------
 debian/patches/config_in_etc.patch                   | 20 --------------------
 debian/patches/python3_explicit.patch                |  8 ++++----
 .../patches/set_absolute_path_to_tex_template.patch  | 17 +++++------------
 4 files changed, 17 insertions(+), 43 deletions(-)

diff --git a/debian/patches/adapt_config.patch b/debian/patches/adapt_config.patch
index cc5ca1e..95f2078 100644
--- a/debian/patches/adapt_config.patch
+++ b/debian/patches/adapt_config.patch
@@ -6,15 +6,16 @@ Description: Use Debian packaged locations
 +++ b/config.txt
 @@ -1,10 +1,10 @@
  [DEFAULT]
--kraken_db =/home/andruscha/programs/kraken/minikraken_20141208/ 
+-kraken_db =/home/andruscha/software/kraken/minikraken_20141208/
 +kraken_db =/var/lib/kraken/minikraken_20141208
- blast_db = /data/BLAST/nt/
  
  [PATH]
--kraken = /home/andruscha/programs/kraken/kraken_build/
--adapter = /data/GS/tools/Trimmomatic-0.32/adapters/
+-kraken =
 +kraken = /usr/lib/kraken
-+adapter = /usr/share/trimmomatic/
- fastqc = /home/lieuv/tools/FastQC/
- trimmomatic =
+ adapter = /data/GS/tools/Trimmomatic-0.32/adapters/
+-fastqc = /home/lieuv/tools/FastQC/
+-trimmomatic =
++fastqc = 
++trimmomatic = /usr/share/trimmomatic/
  bowtie2 =
+ 
diff --git a/debian/patches/config_in_etc.patch b/debian/patches/config_in_etc.patch
index df3509c..9f1b739 100644
--- a/debian/patches/config_in_etc.patch
+++ b/debian/patches/config_in_etc.patch
@@ -18,23 +18,3 @@ Description: Config file should be in /etc/qcumber
  	path_dict = config[section]
  	return path_dict[name]
  
-@@ -36,7 +36,7 @@ class Pipeline:
- 			self.trimmo_version = subprocess.check_output(join(get_tool_path("trimmomatic"), "TrimmomaticSE") + " -version", shell=True).decode("utf-8")
- 		except:
- 			config = configparser.ConfigParser()
--			config.read(join(dirname(__file__), "config.txt"))
-+			config.read(join("/etc/qcumber", "config.txt"))
- 			if "VERSION" in config:
- 				self.trimmo_version = config["VERSION"]["trimmomatic"]
- 			else:
---- a/runQCPipeline.py
-+++ b/runQCPipeline.py
-@@ -448,7 +448,7 @@ def main(arguments):
- 
- if __name__ == "__main__":
- 	config = configparser.ConfigParser()
--	config.read(join(dirname(__file__), "config.txt"))
-+	config.read(join("/etc/qcumber", "config.txt"))
- 	kraken_db = ""
- 	if "DEFAULT" in config:
- 		if "kraken_db" in config["DEFAULT"].keys():
diff --git a/debian/patches/python3_explicit.patch b/debian/patches/python3_explicit.patch
index 9c85c5c..eca80a5 100644
--- a/debian/patches/python3_explicit.patch
+++ b/debian/patches/python3_explicit.patch
@@ -2,11 +2,11 @@ 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/runQCPipeline.py
-+++ b/runQCPipeline.py
+--- a/QCumber.py
++++ b/QCumber.py
 @@ -1,4 +1,4 @@
--#!/usr/bin/env python3.4
+-#!/usr/bin/env python3
 +#!/usr/bin/python3
  # -*- coding: utf-8 -*-
  __author__ = 'LieuV'
- __version__ = "1.1.2"
+ __version__ = "1.0.0"
diff --git a/debian/patches/set_absolute_path_to_tex_template.patch b/debian/patches/set_absolute_path_to_tex_template.patch
index 0474bde..1ad0932 100644
--- a/debian/patches/set_absolute_path_to_tex_template.patch
+++ b/debian/patches/set_absolute_path_to_tex_template.patch
@@ -3,10 +3,10 @@ Last-Update: Wed, 16 Mar 2016 11:01:55 +0100
 Description: Inside the Debian package we know exactly the location of the
  tex template - make sure it will be found reliably
 
---- a/runQCPipeline.py
-+++ b/runQCPipeline.py
-@@ -172,10 +172,11 @@ def writeReport(sample, argMap):
- 	report_name = os.path.join(sample.mainResultsPath,
+--- 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()
@@ -18,13 +18,6 @@ Description: Inside the Debian package we know exactly the location of the
 +	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(argMap["minlen"], argMap["trimOption"], argMap["palindrome"]))
+ 	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")
-@@ -481,4 +482,4 @@ if __name__ == "__main__":
- 	parser.add_argument('-tmp',dest="tmp", required = False, help= "Define Temp folder. Default: output folder.")
- 
- 	arguments = vars(parser.parse_args())
--	main(arguments)
-\ No newline at end of file
-+	main(arguments)

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