[med-svn] [sparta] 04/04: Hack around strange upstream habits

[Andreas Tille]

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tille pushed a commit to branch master
in repository sparta.

commit f257418c2a1faaf8ef5c63cafedb5571effdb02d
Author: Andreas Tille <tille at debian.org>
Date:   Wed Aug 3 10:45:00 2016 +0200

    Hack around strange upstream habits
---
 debian/links                                           |  3 +++
 debian/patches/series                                  |  1 +
 .../stop_fiddling_around_with_system_files.patch       | 18 ++++++++++++++++++
 3 files changed, 22 insertions(+)

diff --git a/debian/links b/debian/links
new file mode 100644
index 0000000..f4b1875
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,3 @@
+usr/bin/fastqc			usr/share/sparta/QC_analysis/FastQC/fastqc
+usr/share/java/trimmomatic.jar	usr/share/sparta/QC_analysis/Trimmomatic-0.33/trimmomatic-0.33.jar
+usr/share/trimmomatic		usr/share/sparta/QC_analysis/Trimmomatic-0.33/adapters
diff --git a/debian/patches/series b/debian/patches/series
index 47d3605..e92b171 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 fix_default_folder_creation.patch
+stop_fiddling_around_with_system_files.patch
diff --git a/debian/patches/stop_fiddling_around_with_system_files.patch b/debian/patches/stop_fiddling_around_with_system_files.patch
new file mode 100644
index 0000000..03c32e8
--- /dev/null
+++ b/debian/patches/stop_fiddling_around_with_system_files.patch
@@ -0,0 +1,18 @@
+--- a/qc_analysis.py
++++ b/qc_analysis.py
+@@ -113,7 +113,7 @@ class QC_analysis(object):
+         if not os.path.isdir(os.path.join(cd.getSPARTAdir(options), "QC_analysis", "FastQC")):
+             subprocess.call(["unzip", "fastqc_v0.11.3.zip"], stdout=open(os.devnull, 'wb'))
+         os.chdir(os.path.join(cd.getSPARTAdir(options), "QC_analysis", "FastQC"))
+-        subprocess.call("chmod 755 fastqc", shell=True)
++        # subprocess.call("chmod 755 fastqc", shell=True)
+         print "FastQC is assessing your data set for overall quality"
+         for file in os.listdir(datalocation):
+             extension = file.split(".")[1]
+@@ -122,4 +122,4 @@ class QC_analysis(object):
+                     subprocess.Popen("./fastqc " + os.path.join(analysislocation, "QC", "trimmed" + file), shell=True).wait()
+                 else:
+                     subprocess.Popen("./fastqc --quiet " + os.path.join(analysislocation, "QC", "trimmed" + file), shell=True).wait()
+-        return
+\ No newline at end of file
++        return

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