[med-svn] [Git][med-team/cct][master] 4 commits: Upload to unstable
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 5 21:52:48 BST 2018
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 <tille at debian.org> Mon, 20 Aug 2018 09:20:03 +0200
+ -- Andreas Tille <tille at 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
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at 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
=====================================
@@ -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 <tille at 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 {
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
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