debian/changelog

-cct (20170919+dfsg-1) UNRELEASED; urgency=medium
+cct (20170919+dfsg-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #908069)
 
- -- Andreas Tille <tille@debian.org>  Mon, 20 Aug 2018 09:20:03 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 05 Sep 2018 21:59:21 +0200

debian/control

@@ -10,7 +10,7 @@ Vcs-Git: https://salsa.debian.org/med-team/cct.git
 Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/
 
 Package: cct
-Architecture: any
+Architecture: all
 Depends: ${perl:Depends},
          ${misc:Depends},
          bioperl,
@@ -34,7 +34,7 @@ Description: visually comparing bacterial, plasmid, chloroplast, or mitochondria
  included with the CCT documentation.
 
 Package: cct-examples
-Architecture: any
+Architecture: all
 Depends: ${perl:Depends},
          ${misc:Depends},
          bioperl,

debian/patches/cgview_path.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 05 Sep 2018 21:59:21 +0200
+Description: Make sure test will work and set correct path to cgview.jar
+
 --- a/conf/global_settings.conf
 +++ b/conf/global_settings.conf
 @@ -44,7 +44,7 @@ myva_file = $cogs_files/myva

debian/patches/debug.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 05 Sep 2018 20:59:49 +0200
+Description: Enable debugging for failed tests
+
 --- a/lib/scripts/local_blast_client/local_blast_client.pl
 +++ b/lib/scripts/local_blast_client/local_blast_client.pl
 @@ -258,8 +258,11 @@ while ( my $sequenceEntry = <SEQFILE> )

debian/patches/series

 cgview_path.patch
 testscripts.patch
-debug.patch
 fix_cgview_path.patch
+# debug.patch

debian/patches/testscripts.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 05 Sep 2018 20:59:49 +0200
+Description: Fix some test scripts regarding pathes and robustness regarding download (s/ftp:/http:/)
+
 --- a/lib/scripts/assign_cogs/test.sh
 +++ b/lib/scripts/assign_cogs/test.sh
-@@ -1,8 +1,9 @@
+@@ -1,8 +1,7 @@
  #!/bin/bash
  set -e
 -formatdb=/usr/local/blast/bin/formatdb
 -scripts_path=/home/paul/stothard_group/projects
+-
 +formatdb=/usr/bin/formatdb
 +scripts_path=/usr/share/cct/lib
  
-+set -x
- 
  wd=`pwd`
  
-@@ -16,11 +17,11 @@ fi
+@@ -16,11 +15,11 @@ fi
  
  cd db
  if [ ! -f myva ]; then
@@ -26,7 +29,7 @@
  fi
  
  if [ ! -f myva.phr ]; then
-@@ -35,7 +36,7 @@ perl assign_cogs.pl -i test_input/sample
+@@ -35,7 +34,7 @@ perl assign_cogs.pl -i test_input/sample
  -get_orfs $scripts_path/get_orfs/get_orfs.pl \
  -get_cds $scripts_path/get_cds/get_cds.pl \
  -local_bl $scripts_path/local_blast_client/local_blast_client.pl \
@@ -35,7 +38,7 @@
  
  perl assign_cogs.pl -i test_input/sample_1.gbk \
  -o test_output/sample_1b.gff -s cds \
-@@ -43,7 +44,7 @@ perl assign_cogs.pl -i test_input/sample
+@@ -43,7 +42,7 @@ perl assign_cogs.pl -i test_input/sample
  -get_orfs $scripts_path/get_orfs/get_orfs.pl \
  -get_cds $scripts_path/get_cds/get_cds.pl \
  -local_bl $scripts_path/local_blast_client/local_blast_client.pl \
@@ -44,7 +47,7 @@
  -a -e 0.0000001 -p 0.60 -v
  
  perl assign_cogs.pl -i test_input/sample_2.fna \
-@@ -52,7 +53,7 @@ perl assign_cogs.pl -i test_input/sample
+@@ -52,7 +51,7 @@ perl assign_cogs.pl -i test_input/sample
  -get_orfs $scripts_path/get_orfs/get_orfs.pl \
  -get_cds $scripts_path/get_cds/get_cds.pl \
  -local_bl $scripts_path/local_blast_client/local_blast_client.pl \
@@ -53,7 +56,7 @@
  
  perl assign_cogs.pl -i test_input/sample_2.fna \
  -o test_output/sample_2b.gff -s orfs \
-@@ -60,7 +61,7 @@ perl assign_cogs.pl -i test_input/sample
+@@ -60,7 +59,7 @@ perl assign_cogs.pl -i test_input/sample
  -get_orfs $scripts_path/get_orfs/get_orfs.pl \
  -get_cds $scripts_path/get_cds/get_cds.pl \
  -local_bl $scripts_path/local_blast_client/local_blast_client.pl \
@@ -62,7 +65,7 @@
  -a -e 0.0000001 -p 0.60 -v
  
  perl assign_cogs.pl -i test_input/sample_3.fna \
-@@ -69,7 +70,7 @@ perl assign_cogs.pl -i test_input/sample
+@@ -69,7 +68,7 @@ perl assign_cogs.pl -i test_input/sample
  -get_orfs $scripts_path/get_orfs/get_orfs.pl \
  -get_cds $scripts_path/get_cds/get_cds.pl \
  -local_bl $scripts_path/local_blast_client/local_blast_client.pl \
@@ -71,6 +74,13 @@
  
  #compare new output to sample output
  new_output=test_output
+@@ -85,4 +84,4 @@ do
+ 	echo "No differences found"
+     fi
+     set -e
+-done
+\ No newline at end of file
++done
 --- a/test.sh
 +++ b/test.sh
 @@ -12,7 +12,7 @@ function abort_test {