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The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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bedtools not found #185

Closed gatoravi closed 9 years ago

gatoravi commented 9 years ago

clinseq fails with this error,

     5 2015-03-30 20:13:26-0500 clia1: bash: bedtools: command not found
     6 2015-03-30 20:13:26-0500 clia1: Command module died or returned undef.
     7 2015-03-30 20:13:26-0500 clia1: ERROR RUNNING COMMAND.  Exit code 127 from: bedtools intersect -a /tmp/1919.tmpdir/gm-genome_sys-2015-03-30_20_13_20--b5Qt/anonymous0 -b /tmp/1919.       tmpdir/gm-genome_sys-2015-03-30_20_13_20--b5Qt/anonymous2 > /opt/gms/MIW3W09/fs/MIW3W09/info/model_data/18177dd5eca44514a47f367d9804e17a/buildd9155c0d0adc4e11a825a483a20f7196/           TST1/cnv/exome_cnv//tumor.normal.ROI.intersect.bed
     8 2015-03-30 20:13:26-0500 clia1: See the command's captured STDERR (if it exists) for more information at /opt/gms/MIW3W09/sw/genome/lib/perl/Genome/Model/Tools/CopyNumber/Cnmops.        pm line 207

We need a newer version, On clia1,

gmsuser@clia1 /opt/gms/MIW3W09/sw/workflow/lib/Workflow/DataSource (gms-pub-2015.02.22)> sudo apt-cache policy bedtools
bedtools:
  Installed: 2.14.3-1
  Candidate: 2.14.3-1
  Version table:
 *** 2.14.3-1 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
        100 /var/lib/dpkg/status

On linus

aramu@linus217 ~>
 bedtools --version
bedtools v2.17.0
gatoravi commented 9 years ago

A new APP dump was created as described here, this was then staged and uploaded to the FTP site. The Makefile was updated to use the updated APPs here

gatoravi commented 9 years ago

An attempt to fix this is here https://github.com/genome/genome/pull/621

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

This has been tested and seems to work fine.