[med-svn] [Git][med-team/kleborate][master] 2 commits: Recommends: python3-biopython to run additional scripts

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kleborate


Commits:
e4516b86 by Andreas Tille at 2019-09-24T14:39:32Z
Recommends: python3-biopython to run additional scripts

- - - - -
845b8cf7 by Andreas Tille at 2019-09-24T14:44:04Z
Enhance patch for Python3 compatibility

- - - - -


2 changed files:

- debian/control
- debian/patches/python3.patch


Changes:

=====================================
debian/control
=====================================
@@ -18,8 +18,9 @@ Package: kleborate
 Architecture: any
 Depends: ${python3:Depends},
          ${misc:Depends},
-         ncbi-blast+ <!nocheck>,
-         mash <!nocheck>
+         ncbi-blast+,
+         mash
+Recommends: python3-biopython
 Description: tool to screen Klebsiella genome assemblies
  Kleborate is a tool to screen Klebsiella genome assemblies for:
  .


=====================================
debian/patches/python3.patch
=====================================
@@ -1,5 +1,6 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Tue, 24 Sep 2019 12:36:03 +0200
+Origin: https://github.com/katholt/Kleborate/issues/17
 Description: When using Python3 the executable is named python3
 
 --- a/kleborate-runner.py
@@ -17,7 +18,7 @@ Description: When using Python3 the executable is named python3
  	# If resistance genes are on, run the resBLAST.py script to get its headers.
  	if args.resistance:
 -		res_out = subprocess.check_output('python ' + resblast +
-+		res_out = subprocess.check_output('python3 ' + resblast +
++		res_out = subprocess.check_output(sys.executable + ' '  + resblast +
  										  ' -s ' + data_folder + '/ARGannot_r2.fasta' +
  										  ' -t ' + data_folder + '/ARGannot_clustered80_r2.csv',
  										  shell=True)
@@ -26,7 +27,7 @@ Description: When using Python3 the executable is named python3
  	kaptive_table = kaptive_prefix + '_table.txt'
  
 -	p = subprocess.Popen('python ' + kaptive_py +
-+	p = subprocess.Popen('python3 ' + kaptive_py +
++	p = subprocess.Popen(sys.executable + ' '  + kaptive_py +
  						 ' -a ' + contigs +
  						 ' -k ' + kaptive_db +
  						 ' -o ' + kaptive_prefix +
@@ -35,7 +36,7 @@ Description: When using Python3 the executable is named python3
  
  def get_chromosome_mlst_results(mlstblast, data_folder, contigs):
 -	f = os.popen('python ' + mlstblast +
-+	f = os.popen('python3 ' + mlstblast +
++	f = os.popen(sys.executable + ' '  + mlstblast +
  				 ' -s ' + data_folder + '/Klebsiella_pneumoniae.fasta' +
  				 ' -d ' + data_folder + '/kpneumoniae.txt' +
  				 ' -i no' +
@@ -44,7 +45,7 @@ Description: When using Python3 the executable is named python3
  								  vir_name, vir_st_name, unknown_group_name, min_gene_count,
  								  header_function):
 -	f = os.popen('python ' + mlstblast +
-+	f = os.popen('python3 ' + mlstblast +
++	f = os.popen(sys.executable + ' '  + mlstblast +
  				 ' -s ' + data_folder + '/' + alleles_fasta +
  				 ' -d ' + data_folder + '/' + profiles_txt +
  				 ' -i yes' +
@@ -53,7 +54,7 @@ Description: When using Python3 the executable is named python3
  def get_hypermucoidy_results(rmpablast, data_folder, contigs):
  	hypermucoidy = '-'
 -	f = os.popen('python ' + rmpablast +
-+	f = os.popen('python3 ' + rmpablast +
++	f = os.popen(sys.executable + ' '  + rmpablast +
  				 ' -s ' + data_folder + '/hypermucoidy.fasta' +
  				 ' -d ' + data_folder + '/hypermucoidy_rmpA.txt' +
  				 ' ' + contigs)
@@ -62,7 +63,7 @@ Description: When using Python3 the executable is named python3
  def get_wzi_and_k_locus_results(mlstblast, data_folder, contigs):
  	wzi_st, k_type = '-', '-'
 -	f = os.popen('python ' + mlstblast +
-+	f = os.popen('python3 ' + mlstblast +
++	f = os.popen(sys.executable + ' '  + mlstblast +
  				 ' -s ' + data_folder + '/wzi.fasta' +
  				 ' -d ' + data_folder + '/wzi.txt' +
  				 ' -i yes' +
@@ -71,7 +72,7 @@ Description: When using Python3 the executable is named python3
  	res_hits = []
  	if args.resistance:
 -		f = os.popen('python ' + resblast +
-+		f = os.popen('python3 ' + resblast +
++		f = os.popen(sys.executable + ' '  + resblast +
  					 ' -s ' + data_folder + '/ARGannot_r2.fasta' +
  					 ' -t ' + data_folder + '/ARGannot_clustered80_r2.csv' +
  					 ' -q ' + data_folder + '/QRDR_120.aa' +



View it on GitLab: https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0

-- 
View it on GitLab: https://salsa.debian.org/med-team/kleborate/compare/44ecf104d5ce95dd8e9b9633dd13eb9ce3a7d3e3...845b8cf7d51825c6c8568444993444dc78342cb0
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