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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
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50 50
51 Read more about the "Phone Home" problem at: 51 Read more about the "Phone Home" problem at:
52 http://www.broadinstitute.org/gatk/guide/article?id=1250 52 http://www.broadinstitute.org/gatk/guide/article?id=1250
53 53
54 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file: 54 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file:
55 ::
56 <tool_dependency_dir>/gatk2/default/env.sh
55 57
56 <tool_dependency_dir>/gatk2/default/env.sh 58 Note that due to the manual nature of the GATK2 installation you will be getting the
59 following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph):
60 ::
61 Failed to resolve dependency on 'gatk2', ignoring.
62
63 This is because the
64 ::
65 <requirement type="package">gatk2</requirement>
66 is specified but never resolved in the tool_dependencies.xml. It is safe to ignore.
57 67
58 Finally, you should fill in additional information about your genomes and 68 Finally, you should fill in additional information about your genomes and
59 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. 69 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt.
60 You can find them in the tool-data/ Galaxy directory. 70 You can find them in the tool-data/ Galaxy directory.
61
62 71
63 History 72 History
64 ======= 73 =======
65 74
66 * v0.1 - Initial public release 75 * v0.1 - Initial public release