debian/changelog

 sspace (2.1.1+dfsg-5) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * Use 2to3 to port to Python3
     Closes: #938565
   * debhelper-compat 12
-  * Standards-Version: 4.4.0
   * Remove trailing whitespace in debian/changelog
   * Fix permission of fasta file
 
+  [ Sascha Steinbiss ]
+  * Bump Standards-Version.
+
  -- Andreas Tille <tille@debian.org>  Fri, 06 Sep 2019 12:03:56 +0200
 
 sspace (2.1.1+dfsg-4) unstable; urgency=medium

debian/control

@@ -6,10 +6,10 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
                recode,
-               python,
+               python3,
                asciidoctor,
                bowtie
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/sspace
 Vcs-Git: https://salsa.debian.org/med-team/sspace.git
 Homepage: https://github.com/nsoranzo/sspace_basic

debian/patches/debug.patch

---- a/bin/PairingAndScaffolding.pl
-+++ b/bin/PairingAndScaffolding.pl
-@@ -821,7 +821,7 @@ sub mapReadsWithBowtie{
-    my $procline = "bowtie -p $threads -v $gaps -m 1 bowtieoutput/$bowtieout --suppress 6,7 -f $singlereads --quiet --refidx |";
-    die "Contig file ($contigFile) not found. Exiting...\n" if(!(-e $contigFile));
-    &printMessage("\n=>".getDate().": Building Bowtie index for contigs\n");
--   system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error; $?"; # returns exit status values
-+   system("bowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref") == 0 || die "\nBowtie-build error\n\tbowtie-build $contigFile bowtieoutput/$bowtieout --quiet --noref; $?"; # returns exit status values
-    
-    #Treat the output of Bowtie differently if multithreading is used or not
-    readBowtieOneThread($procline) if($threads <= 1);

debian/patches/series

 shebangs.patch
 2to3.patch
-debug.patch

debian/tests/example-tests

@@ -17,12 +17,6 @@ else
   CMD=sspace
 fi
 
-set -x
-which python
-python
-which bowtie-build
-bowtie-build --help
-ls -l
 $CMD -l libraries.txt -s contigs_abyss.fasta
 
 [ -s standard_output.final.evidence ]