debian/cwl-runner/cwl-runner

+#!/home/dabrowskiw/cwl/cwl_vw/bin/python3
+
+# -*- coding: utf-8 -*-
+import re
+import sys
+
+from cwltool.main import main
+
+if __name__ == '__main__':
+    sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])
+    sys.exit(main())

debian/patches/path_to_report.tex.patch

+--- a/mapping.py
++++ b/mapping.py
+@@ -134,10 +134,10 @@ class MAPPING:
+         # self.env = jinja2.Environment()
+         # self.env.loader = jinja2.FileSystemLoader('.')
+ 
+-        # self.template = self.env.get_template(os.path.join(os.path.dirname(__file__), 'report.tex'))
++        # self.template = self.env.get_template(os.path.join('/usr/share/mapping-pipeline', 'report.tex'))
+         # self.pdf_latex = self.template.render(pipeline=self, metric=self.metric)
+         template_dir = os.path.dirname(__file__) #'/usr/share/mapping-pipeline'
+-        template_file = 'report.tex'
++        template_file = '/usr/share/mapping-pipeline/report.tex'
+         loader = jinja2.FileSystemLoader(template_dir)
+         env = jinja2.Environment(loader=loader)
+         template = env.get_template(template_file)

debian/patches/picard.patch

+--- a/mapping.py
++++ b/mapping.py
+@@ -390,7 +390,7 @@ class MAPPING:
+         self.args.reference = files
+ 
+     def _valid_picard(self, f):
+-        if os.path.isfile(os.path.join(os.path.realpath(f), 'picard.jar')):
++        if os.path.isfile(os.path.join('/usr/share/java', 'picard.jar')):
+             return f
+         else:
+             raise argparse.ArgumentTypeError('Cannot find picard.jar in folder {}'.format(os.path.realpath(f)))

debian/patches/python3.patch

@@ -7,14 +7,12 @@ Description: This script should not be called directly
 
 --- a/metrics.py
 +++ b/metrics.py
-@@ -1,6 +1,4 @@
+@@ -1,5 +1,3 @@
 -#!/usr/bin/env python
 -
--import custom_logger as log
-+from . import custom_logger as log
+ import custom_logger as log
  import numpy as np
  import matplotlib
- matplotlib.use('Agg')
 @@ -120,7 +118,7 @@ class METRICS:
                  self.reads_per_quality_result.append([os.path.realpath(os.path.join(self.output, 'reads_per_quality_{}.pdf'.format(valid_filename(reference)))), reference.replace('_','\_')])
                  fig, ax = plt.subplots( nrows=1, ncols=1 )  # create figure & 1 axis

debian/patches/series

 python3.patch
 config.patch
+picard.patch
+path_to_report.tex.patch

debian/rules

@@ -10,5 +10,5 @@ override_dh_fixperms:
 	find debian -name "*.tex" -exec chmod -x \{\} \;
 	find debian -name "*.json" -exec chmod -x \{\} \;
 	for py in `find debian -name "*.py"` ; do \
-	    if ! head -n 1 $$py | grep -q '^#!/usr/bin/python' ; then chmod -x $$py ; fi ; \
+	    if ! head -n 1 $$py | grep -q '^#! */usr/bin/.*python' ; then chmod -x $$py ; fi ; \
 	done