[med-svn] [qcumber] 03/06: New upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 330c59396000d939927b27438e3d412a79246628
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 13 14:27:19 2017 +0100

    New upstream version
---
 debian/changelog                                       |  6 ++++++
 debian/patches/adapt_config.patch                      |  9 ++++-----
 debian/patches/check_fasta.patch                       | 16 ++++++++--------
 debian/patches/set_absolute_path_to_tex_template.patch |  8 ++++----
 4 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 976a790..3a6905b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+qcumber (1.0.9+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Mon, 13 Mar 2017 14:27:04 +0100
+
 qcumber (1.0.5+dfsg-2) unstable; urgency=medium
 
   * Check reference file for valid fasta
diff --git a/debian/patches/adapt_config.patch b/debian/patches/adapt_config.patch
index 8218e6d..75f0739 100644
--- a/debian/patches/adapt_config.patch
+++ b/debian/patches/adapt_config.patch
@@ -6,15 +6,14 @@ Description: Use Debian packaged locations
 +++ b/config.txt
 @@ -1,10 +1,10 @@
  [DEFAULT]
--kraken_db =/opt/common/pipelines/databases/minikraken_20141208/
+-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/
+ kraken =
+-adapter = /opt/common/pipelines/tools/Trimmomatic-0.36/adapters/
 -fastqc = /opt/common/pipelines/tools/FastQC_0.11.5/
--trimmomatic =
-+kraken = /usr/lib/kraken
+-trimmomatic = /opt/common/pipelines/tools/Trimmomatic-0.36/
 +adapter = /usr/share/trimmomatic/
 +fastqc = 
 +trimmomatic = /usr/bin
diff --git a/debian/patches/check_fasta.patch b/debian/patches/check_fasta.patch
index cd807ee..2c39f63 100644
--- a/debian/patches/check_fasta.patch
+++ b/debian/patches/check_fasta.patch
@@ -1,8 +1,8 @@
 --- a/QCumber.py
 +++ b/QCumber.py
-@@ -29,6 +29,24 @@ r1_pattern = parameter["Pattern"]["R1"]
- r2_pattern = parameter["Pattern"]["R2"]
- lane_pattern = parameter["Pattern"]["lane"]
+@@ -32,6 +32,24 @@ global r2_pattern
+ global sep_pattern
+ global lane_pattern
  
 +from sys import stderr
 +from Bio import SeqIO
@@ -22,10 +22,10 @@
 +		print('%s %s does not contain valid fasta data' % (filetype, fastafile), file=stderr)
 +		return False
 +
- def get_illumina_reads(  output, tmp):
- 	## Add readsets to sample
+ def get_illumina_reads(tmp):
  	readsets = []
-@@ -271,8 +289,8 @@ def main(arguments):
+ 
+@@ -232,8 +250,8 @@ def check_input_validity():
  		if not arguments["reference"]:
  			sys.exit("Mapping needs a reference.")
  		else:
@@ -34,5 +34,5 @@
 +			if not check_fasta(arguments["reference"],"Reference"):
 +				sys.exit(1)
  
- 	if not arguments["nokraken"]:
- 		if not os.path.exists(arguments["db"]):
+ 	#
+ 	#Check validity of Kraken DB
diff --git a/debian/patches/set_absolute_path_to_tex_template.patch b/debian/patches/set_absolute_path_to_tex_template.patch
index 67d53a0..48a9178 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/QCumber.py
 +++ b/QCumber.py
-@@ -168,10 +168,11 @@ def writeReport(sample, arguments):
+@@ -180,10 +180,11 @@ def writeReport(sample):
  	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)
@@ -18,6 +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(arguments["palindrome"],arguments["minlen"], arguments["trimOption"]))
- 
- 	latex = open(report_name + ".tex", "w")
+ 	try:
+ 		trim_param= sample.readSets[0].trimRes.print_param(arguments["palindrome"], arguments["minlen"], arguments["trimOption"])
+ 	except:

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