Andreas Tille pushed to branch master at Debian Med / cct
Commits: c0e42754 by Andreas Tille at 2018-09-05T19:59:35Z Upload to unstable - - - - - 0f849387 by Andreas Tille at 2018-09-05T20:29:09Z DEP3 - - - - - 70dc6e6e by Andreas Tille at 2018-09-05T20:50:24Z Arch: all - - - - - 1177a8fd by Andreas Tille at 2018-09-05T20:51:50Z DEP3 - - - - - 6 changed files: - debian/changelog - debian/control - debian/patches/cgview_path.patch - debian/patches/debug.patch - debian/patches/series - debian/patches/testscripts.patch Changes: ===================================== debian/changelog ===================================== @@ -1,5 +1,5 @@ -cct (20170919+dfsg-1) UNRELEASED; urgency=medium +cct (20170919+dfsg-1) unstable; urgency=medium - * Initial release (Closes: #<bug>) + * Initial release (Closes: #908069) - -- Andreas Tille <[email protected]> Mon, 20 Aug 2018 09:20:03 +0200 + -- Andreas Tille <[email protected]> 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 ===================================== @@ -1,3 +1,7 @@ +Author: Andreas Tille <[email protected]> +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 ===================================== @@ -1,3 +1,7 @@ +Author: Andreas Tille <[email protected]> +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 ===================================== @@ -1,4 +1,4 @@ cgview_path.patch testscripts.patch -debug.patch fix_cgview_path.patch +# debug.patch ===================================== debian/patches/testscripts.patch ===================================== @@ -1,18 +1,21 @@ +Author: Andreas Tille <[email protected]> +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 { View it on GitLab: https://salsa.debian.org/med-team/cct/compare/e859d17791f1f01895dc11c8920d4c8b4db71fce...1177a8fd27f68a92386a5acb4906673336fdf02d -- View it on GitLab: https://salsa.debian.org/med-team/cct/compare/e859d17791f1f01895dc11c8920d4c8b4db71fce...1177a8fd27f68a92386a5acb4906673336fdf02d You're receiving this email because of your account on salsa.debian.org.
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