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genome / gms

The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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missing cufflinks version. #183

Closed gatoravi closed 9 years ago

gatoravi commented 9 years ago

Differential expression fails with,

     1 2015-03-27 21:00:17-0500 clia1: Command module died or returned undef.
     2 2015-03-27 21:00:17-0500 clia1: No path for cufflinks version 2.1.1 at /opt/gms/MIW3W09/sw/genome/lib/perl/Genome/Model/Tools/                Cufflinks.pm line 114, <GEN10> line 1936705.
     3 2015-03-27 21:00:17-0500 clia1:   Genome::Model::Tools::Cufflinks::path_for_cufflinks_version('Genome::Model::Tools::Cufflinks::              Cuffcompare=HASH(0x72fd390)', 2.1.1) called at /opt/gms/MIW3W09/sw/genome/lib/perl/Genome/Model/Tools/Cufflinks.pm line 92
     4 2015-03-27 21:00:17-0500 clia1:   Genome::Model::Tools::Cufflinks::__ANON__('Genome::Model::Tools::Cufflinks::                                Cuffcompare=HASH(0x72fd390)') called at /opt/gms/MIW3W09/sw/genome/lib/perl/Genome/Model/Tools/Cufflinks/Cuffcompare.pm line 108
gatoravi commented 9 years ago

this is addressed here, https://github.com/genome/genome-snapshot-deps/pull/26

gatoravi commented 9 years ago

This is fixed now, we need to test this on a fresh install before closing.

gatoravi commented 9 years ago

Cufflinks is now installed succesfully,

gmsuser@clia1 ~/gms (ubuntu-12.04-2015.02.22)> which cufflinks2.1.1
/usr/bin/cufflinks2.1.1