[med-svn] [Git][med-team/cct][master] 2 commits: Set path to cgview.jar

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / cct


Commits:
2e9f092c by Andreas Tille at 2018-08-20T20:43:15Z
Set path to cgview.jar

- - - - -
25ac23fb by Andreas Tille at 2018-08-20T20:43:34Z
Add some debug code - Somehow the call to blastall / blastp is broken ...

- - - - -


3 changed files:

- + debian/patches/cgview_path.patch
- + debian/patches/debug.patch
- debian/patches/series


Changes:

=====================================
debian/patches/cgview_path.patch
=====================================
--- /dev/null
+++ b/debian/patches/cgview_path.patch
@@ -0,0 +1,11 @@
+--- a/conf/global_settings.conf
++++ b/conf/global_settings.conf
+@@ -44,7 +44,7 @@ myva_file = $cogs_files/myva
+ 
+ cgview_xml_builder = $comparison_tool/lib/scripts/cgview_xml_builder/cgview_xml_builder.pl
+ 
+-cgview = $comparison_tool/bin/cgview.jar
++cgview = /usr/share/java/cgview.jar
+ 
+ project_settings = $comparison_tool/conf/project_settings.conf
+ 


=====================================
debian/patches/debug.patch
=====================================
--- /dev/null
+++ b/debian/patches/debug.patch
@@ -0,0 +1,14 @@
+--- 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> )
+ 
+     print
+         "Performing BLAST search for sequence number $seqCount ($sequenceTitle).\n";
++    print "DEBUG: $blast_command\ncontent of $filename is:\n";
++    `cat $filename` ;
+ 
+     my $result = `$blast_command`;
++    print "DEBUG: result = $result\n";
+ 
+     my $hitFound = 0;
+     my $HSPCount = 0;


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
+cgview_path.patch
 testscripts.patch
+debug.patch



View it on GitLab: https://salsa.debian.org/med-team/cct/compare/04e15a497e277af21c2fdd37760951712f199249...25ac23fb93dcfa4d6731c0e46d57327974acbdf8

-- 
View it on GitLab: https://salsa.debian.org/med-team/cct/compare/04e15a497e277af21c2fdd37760951712f199249...25ac23fb93dcfa4d6731c0e46d57327974acbdf8
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