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 You're receiving this email because of your account on salsa.debian.org.
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