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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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Can't locate File/Touch.pm in @INC #180

Closed gatoravi closed 9 years ago

gatoravi commented 9 years ago

Add Perl dependency to precise as added here to lucid. https://github.com/genome/genome-snapshot-deps/commit/76308608db7418b59c10804481c9a2fd5f72c4c3

gatoravi commented 9 years ago 
sudo apt-get install libfile-touch-perl

ubuntu@ip-172-31-19-86 /opt/gms/RGTBV26/sw/workflow/lib/Workflow (gms-pub-2015.02.22)> apt-cache policy libfile-touch-perl
libfile-touch-perl:
  Installed: 0.08-1
  Candidate: 0.08-1
  Version table:
 *** 0.08-1 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
        100 /var/lib/dpkg/status

Manually installing the module seems to have worked, we just need to add this to the apt-dependencies and create a new APT dump as documented here

gatoravi commented 9 years ago

a new APT dump with this module was just uploaded, this will needed to be tested.

Uploading to precise-genome-development (via scp to repo.gsc.wustl.edu):
aramu@repo.gsc.wustl.edu's password:
genome-snapshot-deps_2015.03.23-1~Ubuntu~precise.dsc                                                                                                        100% 1361     1.3KB/s   00:00
genome-snapshot-deps_2015.03.23-1~Ubuntu~precise.tar.gz                                                                                                     100%  598KB 598.3KB/s   00:00
genome-snapshot-deps-apps-external_2015.03.23-1~Ubuntu~precise_all.deb                                                                                      100% 6846     6.7KB/s   00:00
genome-snapshot-deps-apps-tgi_2015.03.23-1~Ubuntu~precise_all.deb                                                                                           100% 6494     6.3KB/s   00:00
genome-snapshot-deps-perl_2015.03.23-1~Ubuntu~precise_all.deb                                                                                               100% 8870     8.7KB/s   00:00
genome-snapshot-deps-python_2015.03.23-1~Ubuntu~precise_all.deb                                                                                             100% 6166     6.0KB/s   00:00
genome-snapshot-deps-refcov_2015.03.23-1~Ubuntu~precise_all.deb                                                                                             100% 6546     6.4KB/s   00:00
genome-snapshot-deps-trans-abyss_2015.03.23-1~Ubuntu~precise_all.deb                                                                                        100% 6204     6.1KB/s   00:00
genome-snapshot-deps-ur_2015.03.23-1~Ubuntu~precise_all.deb                                                                                                 100% 6502     6.4KB/s   00:00
genome-snapshot-deps-workflow_2015.03.23-1~Ubuntu~precise_all.deb                                                                                           100% 6374     6.2KB/s   00:00
genome-snapshot-deps_2015.03.23-1~Ubuntu~precise_all.deb                                                                                                    100% 6170     6.0KB/s   00:00
genome-snapshot-deps_2015.03.23-1~Ubuntu~precise_amd64.changes                                                                                              100% 6141     6.0KB/s   00:00
aramu@repo.gsc.wustl.edu's password:
Successfully uploaded packages.
aramu@repo.gsc.wustl.edu's password:
Exporting indices...
Deleting files no longer referenced...
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-apps-external_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-apps-tgi_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-perl_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-python_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-refcov_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-trans-abyss_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-ur_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps-workflow_2015.03.08-1~Ubuntu~precise_all.deb
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps_2015.03.08-1~Ubuntu~precise.dsc
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps_2015.03.08-1~Ubuntu~precise.tar.gz
deleting and forgetting pool/main/g/genome-snapshot-deps/genome-snapshot-deps_2015.03.08-1~Ubuntu~precise_all.deb
gatoravi commented 9 years ago

A commit to use this APT dump is here https://github.com/genome/gms/commit/c38a559337562695ced51b995abcb7b62208bb41

This is now being installed correctly,

gmsuser@clia1 ~/gms (ubuntu-12.04-2015.02.22)> apt-cache policy libfile-touch-perl
libfile-touch-perl:
  Installed: 0.08-1
  Candidate: 0.08-1
  Version table:
 *** 0.08-1 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
        100 /var/lib/dpkg/status

closing this.