fasta_clipping_histogram missing GD/Graph/bars.pm

[sarah-peter]

What would be the suggested way to fix this? Tool and dependency are coming from the toolshed, so technically the package_fastx_toolkit_0_0_13 would need to include the GD::Graph::bars perl module as a dependency.

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job id: 45533
tool id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_clipping_histogram/cshl_fasta_clipping_histogram/1.0.0
tool version: 1.0.0
job pid or drm id: 1432
job tool version:

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job command line:
fasta_clipping_histogram.pl /export/galaxy-central/database/files/057/dataset_57088.dat /export/galaxy-central/database/files/057/dataset_57089.dat

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job stderr:
Can't locate GD/Graph/bars.pm in @inc (you may need to install the GD::Graph::bars module) (@inc contains: /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /galaxy-central/tool_deps/fastx_toolkit/0.0.13/devteam/package_fastx_toolkit_0_0_13/ec66ae4c269b/bin/fasta_clipping_histogram.pl line 21.
BEGIN failed--compilation aborted at /galaxy-central/tool_deps/fastx_toolkit/0.0.13/devteam/package_fastx_toolkit_0_0_13/ec66ae4c269b/bin/fasta_clipping_histogram.pl line 21.

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[sarah-peter]

Of course just installing the perl module doesn't work, because it needs the libgd-dev package (which again has a ton of dependencies). And even then it seems GD.pm doesn't like to be installed in a non-standard location.

[gongbinsheng]

Hi diehlsa,
I've got the same problem. Do you have any solution for that? Our galaxy is running on a cluster.

[bgruening]

Conda as dependency mechanism should solve this problem once and for all. I have started to port fastx to conda here, any help appreciated: galaxyproject/tools-devteam#375