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The Genome Modeling System installer
https://github.com/genome/gms/wiki
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gmt --help fails with perl autoloading error for Math/Combinatorics.pm #137

Closed malachig closed 10 years ago

malachig commented 10 years ago

Getting the following error in the sGMS but not within TGI.

gmt --help

ERROR: Error while autoloading with 'use Genome::Model::Tools::Sciclone': Can't locate Math/Combinatorics.pm in @INC (@INC contains: /opt/gms/0HDDD95/sw/ur/lib /opt/gms/0HDDD95/sw/workflow/lib /opt/gms/0HDDD95/sw/genome/lib/perl/x86_64-linux-gnu-thread-multi /opt/gms/0HDDD95/sw/genome/lib/perl /opt/gms/0HDDD95/sw/genome/lib/perl-added /usr/lib/perl5/x86_64-linux-gnu-thread-multi /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14.2 /usr/share/perl/5.14.2 /usr/local/lib/site_perl /vagrant) at /opt/gms/0HDDD95/sw/genome/lib/perl/Genome/Model/Tools/Sciclone.pm line 9.
BEGIN failed--compilation aborted at /opt/gms/0HDDD95/sw/genome/lib/perl/Genome/Model/Tools/Sciclone.pm line 9.
Compilation failed in require at (eval 2348) line 2.
BEGIN failed--compilation aborted at (eval 2348) line 2.
 at /opt/gms/0HDDD95/sw/genome/bin/gmt line 25

@chrisamiller do you by chance know how Math::Combinatorics used by Genome::Model::Tools::Sciclone is installed?

ghost commented 10 years ago

On my workstation, Math::Combinatorics is installed at /usr/share/perl5/Math/Combinatorics.pm. That file was installed by the libmath-combinatorics-perl package.

malachig commented 10 years ago

Looks like this was added to genome-snapshot-deps for lucid but not precise:

cd /gscuser/mgriffit/git/genome/genome-snapshot-deps
git submodule update --init genome-snapshot-deps
grep -R -i combinatorics *
lucid/changelog:  * [34f1610] add libmath-combinatorics-perl (>= 0.09-3)
lucid/genome-snapshot-deps-perl.depends:libmath-combinatorics-perl (>= 0.09-3)
malachig commented 10 years ago

On an sGMS system:

sudo apt-cache policy libmath-combinatorics-perl

libmath-combinatorics-perl:
  Installed: (none)
  Candidate: 0.09-4
  Version table:
     0.09-4 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

Installation seems to work:

sudo apt-get install libmath-combinatorics-perl

Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following NEW packages will be installed:
  libmath-combinatorics-perl
0 upgraded, 1 newly installed, 0 to remove and 128 not upgraded.
Need to get 18.2 kB of archives.
After this operation, 86.0 kB of additional disk space will be used.
Get:1 http://us.archive.ubuntu.com/ubuntu/ precise/universe libmath-combinatorics-perl all 0.09-4 [18.2 kB]
Fetched 18.2 kB in 0s (167 kB/s)                      
Selecting previously unselected package libmath-combinatorics-perl.
(Reading database ... 174676 files and directories currently installed.)
Unpacking libmath-combinatorics-perl (from .../libmath-combinatorics-perl_0.09-4_all.deb) ...
Processing triggers for man-db ...
Setting up libmath-combinatorics-perl (0.09-4) ...

After installation:

sudo apt-cache policy libmath-combinatorics-perl

libmath-combinatorics-perl:
  Installed: 0.09-4
  Candidate: 0.09-4
  Version table:
 *** 0.09-4 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
        100 /var/lib/dpkg/status
malachig commented 10 years ago

To fix this issue we need to add libmath-combinatorics-perl to genome-snapshot-deps for precise, update the changelog, publish to the APT repository, and update our APT dump. @gatoravi as you have done this several times recently, can you please take this one.

gatoravi commented 10 years ago

ok great, adding this now.

gatoravi commented 10 years ago

genome-snapshot-ceps was updated and a new APT dump(2014.03.31) was created which contains 'libmath-combinatorics-perl'. This APT dump was tested on a VM and works fine.

vagrant@precise64 /vagrant (ubuntu-12.04)> perl -e 'use Math::Combinatorics'
vagrant@precise64 /vagrant (ubuntu-12.04)> apt-cache policy libmath-combinatorics-perl
libmath-combinatorics-perl:
  Installed: 0.09-4
  Candidate: 0.09-4
  Version table:
 *** 0.09-4 0
        990 http://us.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
        100 /var/lib/dpkg/status
gatoravi commented 10 years ago

gmt --help also works fine, closing this issue for now.