[med-svn] [qcumber] 06/15: Fix directory names

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 910be6cc9e8943ffaf0fea1967d0062ba1e52913
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 21 17:54:07 2016 +0200

    Fix directory names
---
 debian/doc-base                                        | 15 ---------------
 debian/install                                         |  8 ++++----
 debian/links                                           |  2 +-
 debian/patches/config_in_etc.patch                     | 10 +++++-----
 debian/patches/set_absolute_path_to_tex_template.patch |  2 +-
 debian/rules                                           |  3 ++-
 6 files changed, 13 insertions(+), 27 deletions(-)

diff --git a/debian/doc-base b/debian/doc-base
deleted file mode 100644
index a3a8051..0000000
--- a/debian/doc-base
+++ /dev/null
@@ -1,15 +0,0 @@
-Document: qc-pipeline
-Title: QCpipeline
-Author: Vivi Lieu <LieuV at rki.de>
-Abstract:  quality control of genomic sequences
- QCPipeline is a tool for quality control. The workflow is as followed:
- .
-  1. Quality control with FastQC
-  2. Trim Reads with Trimmomatic
-  3. Quality control of trimmed reads with FastQC
-  4. Map reads against reference using bowtie2
-  5. Classify reads with Kraken
-Section: Science/Biology
-
-Format: pdf
-Files: /usr/share/doc/qc-pipeline/QC_Pipeline.pdf
diff --git a/debian/install b/debian/install
index ffc4b6e..da73614 100644
--- a/debian/install
+++ b/debian/install
@@ -1,4 +1,4 @@
-*.py		usr/share/qc-pipeline
-config.txt	etc/qc-pipeline
-parameter.txt	etc/qc-pipeline
-*.tex		usr/share/qc-pipeline
+*.py		usr/share/qcumber
+config.txt	etc/qcumber
+parameter.txt	etc/qcumber
+*.tex		usr/share/qcumber
diff --git a/debian/links b/debian/links
index 1e99dfc..a9257e0 100644
--- a/debian/links
+++ b/debian/links
@@ -1 +1 @@
-usr/share/qc-pipeline/runQCPipeline.py	usr/bin/runQCPipeline
+usr/share/qcumber/runQCPipeline.py	usr/bin/runQCPipeline
diff --git a/debian/patches/config_in_etc.patch b/debian/patches/config_in_etc.patch
index f14b8c3..3cd2b60 100644
--- a/debian/patches/config_in_etc.patch
+++ b/debian/patches/config_in_etc.patch
@@ -1,6 +1,6 @@
 Author: Andreas Tille <TilleA at rki.de>
 Last-Update: Wed, 16 Mar 2016 11:01:55 +0100
-Description: Config file should be in /etc/qc-pipeline
+Description: Config file should be in /etc/qcumber
 
 --- a/classes.py
 +++ b/classes.py
@@ -9,12 +9,12 @@ Description: Config file should be in /etc/qc-pipeline
  
  default_parameter = configparser.ConfigParser()
 -default_parameter.read(join(dirname(__file__), "parameter.txt"))
-+default_parameter.read("/etc/qc-pipeline", "parameter.txt"))
++default_parameter.read("/etc/qcumber", "parameter.txt"))
  
  def get_tool_path(name, section="PATH"):
  	config = configparser.ConfigParser()
 -	config.read(join(dirname(__file__), "config.txt"))
-+	config.read("/etc/qc-pipeline", "config.txt"))
++	config.read("/etc/qcumber", "config.txt"))
  	path_dict = config[section]
  	return path_dict[name]
  
@@ -23,7 +23,7 @@ Description: Config file should be in /etc/qc-pipeline
  		except:
  			config = configparser.ConfigParser()
 -			config.read(join(dirname(__file__), "config.txt"))
-+			config.read("/etc/qc-pipeline", "config.txt"))
++			config.read("/etc/qcumber", "config.txt"))
  			if "VERSION" in config:
  				self.trimmo_version = config["VERSION"]["trimmomatic"]
  			else:
@@ -34,7 +34,7 @@ Description: Config file should be in /etc/qc-pipeline
  if __name__ == "__main__":
  	config = configparser.ConfigParser()
 -	config.read(join(dirname(__file__), "config.txt"))
-+	config.read(join("/etc/qc-pipeline", "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/set_absolute_path_to_tex_template.patch b/debian/patches/set_absolute_path_to_tex_template.patch
index 3df4526..de3ad73 100644
--- a/debian/patches/set_absolute_path_to_tex_template.patch
+++ b/debian/patches/set_absolute_path_to_tex_template.patch
@@ -13,7 +13,7 @@ Description: Inside the Debian package we know exactly the location of the
 -	env.loader = FileSystemLoader(os.path.dirname(__file__))
 -
 -	template = env.get_template("report.tex")
-+	template_dir = '/usr/share/qc-pipeline'
++	template_dir = '/usr/share/qcumber'
 + 	template_file = 'report.tex'
 +	loader = FileSystemLoader(template_dir)
 +	env = Environment(loader=loader)
diff --git a/debian/rules b/debian/rules
index 8b0c283..fb51735 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,8 @@ override_dh_compress:
 override_dh_fixperms:
 	dh_fixperms
 	# main script should be executable
-	chmod a+x debian/*/usr/share/*/runQCPipeline.py
+	chmod a-x debian/*/usr/share/*/*.tex
+	chmod a-x debian/*/etc/*/*.txt
 
 #get-orig-source:
 #	. debian/get-orig-source

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