[med-svn] [qcumber] 03/15: update patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 0efe18c50b2ffab5df2bca060f30d5fd15c85589
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 21 15:49:04 2016 +0200

    update patches
---
 debian/install                                     |  1 +
 debian/patches/adapt_config.patch                  |  7 +++--
 debian/patches/config_in_etc.patch                 | 33 +++++++++++++---------
 .../set_absolute_path_to_tex_template.patch        |  2 +-
 4 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/debian/install b/debian/install
index 4e88ce7..ffc4b6e 100644
--- a/debian/install
+++ b/debian/install
@@ -1,3 +1,4 @@
 *.py		usr/share/qc-pipeline
 config.txt	etc/qc-pipeline
+parameter.txt	etc/qc-pipeline
 *.tex		usr/share/qc-pipeline
diff --git a/debian/patches/adapt_config.patch b/debian/patches/adapt_config.patch
index d9e5fd3..cc5ca1e 100644
--- a/debian/patches/adapt_config.patch
+++ b/debian/patches/adapt_config.patch
@@ -4,16 +4,17 @@ Description: Use Debian packaged locations
 
 --- a/config.txt
 +++ b/config.txt
-@@ -1,9 +1,9 @@
+@@ -1,10 +1,10 @@
  [DEFAULT]
 -kraken_db =/home/andruscha/programs/kraken/minikraken_20141208/ 
-+kraken_db = /var/lib/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 = /usr/lib/kraken
 +adapter = /usr/share/trimmomatic/
- fastqc = 
+ fastqc = /home/lieuv/tools/FastQC/
  trimmomatic =
  bowtie2 =
diff --git a/debian/patches/config_in_etc.patch b/debian/patches/config_in_etc.patch
index b4a2537..f14b8c3 100644
--- a/debian/patches/config_in_etc.patch
+++ b/debian/patches/config_in_etc.patch
@@ -4,27 +4,32 @@ Description: Config file should be in /etc/qc-pipeline
 
 --- a/classes.py
 +++ b/classes.py
-@@ -15,7 +15,7 @@ import shutil
- def get_tool_path(name):
+@@ -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("/etc/qc-pipeline", "parameter.txt"))
+ 
+ def get_tool_path(name, section="PATH"):
  	config = configparser.ConfigParser()
 -	config.read(join(dirname(__file__), "config.txt"))
-+	config.read(join("/etc/qc-pipeline", "config.txt"))
- 	path_dict = config["PATH"]
++	config.read("/etc/qc-pipeline", "config.txt"))
+ 	path_dict = config[section]
  	return path_dict[name]
  
-@@ -32,7 +32,7 @@ class Pipeline:
- 		self.fastqc_version = toLatex(subprocess.check_output(join(get_tool_path("fastqc"), "fastqc") + " --version", shell = True).decode("utf-8"))
- 
- 		config = configparser.ConfigParser()
--		config.read(join(dirname(__file__), "config.txt"))
-+		config.read(join("/etc/qc-pipeline", "config.txt"))
- 		if "VERSION" in config:
- 			self.trimmo_version = config["VERSION"]["trimmomatic"]
- 		else:
+@@ -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("/etc/qc-pipeline", "config.txt"))
+ 			if "VERSION" in config:
+ 				self.trimmo_version = config["VERSION"]["trimmomatic"]
+ 			else:
 --- a/runQCPipeline.py
 +++ b/runQCPipeline.py
-@@ -203,7 +203,7 @@ def check_project(argMap):
+@@ -448,7 +448,7 @@ def main(arguments):
  
  if __name__ == "__main__":
  	config = configparser.ConfigParser()
diff --git a/debian/patches/set_absolute_path_to_tex_template.patch b/debian/patches/set_absolute_path_to_tex_template.patch
index 0fd6a35..3df4526 100644
--- a/debian/patches/set_absolute_path_to_tex_template.patch
+++ b/debian/patches/set_absolute_path_to_tex_template.patch
@@ -5,7 +5,7 @@ Description: Inside the Debian package we know exactly the location of the
 
 --- a/runQCPipeline.py
 +++ b/runQCPipeline.py
-@@ -154,10 +154,11 @@ def writeReport(sample, argMap):
+@@ -172,10 +172,11 @@ def writeReport(sample, argMap):
  	report_name = os.path.join(sample.mainResultsPath,
  		 "summary_" + sample.name + "_" + datetime.datetime.strftime(datetime.datetime.now(), "%d-%m-%y_%H-%M"))
  	print("Writing latex " ,report_name)

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