Mercurial > repos > iuc > gatk2
changeset 12:86007c982f00 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
| author | iuc |
|---|---|
| date | Thu, 14 May 2015 22:47:18 -0400 |
| parents | 0d369d08ad6e |
| children | 669a23f1f4b5 |
| files | readme.rst |
| diffstat | 1 files changed, 11 insertions(+), 2 deletions(-) [+] |
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--- a/readme.rst Mon May 04 22:47:06 2015 -0400 +++ b/readme.rst Thu May 14 22:47:18 2015 -0400 @@ -52,14 +52,23 @@ http://www.broadinstitute.org/gatk/guide/article?id=1250 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file: +:: + <tool_dependency_dir>/gatk2/default/env.sh -<tool_dependency_dir>/gatk2/default/env.sh +Note that due to the manual nature of the GATK2 installation you will be getting the +following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph): +:: + Failed to resolve dependency on 'gatk2', ignoring. + +This is because the +:: + <requirement type="package">gatk2</requirement> +is specified but never resolved in the tool_dependencies.xml. It is safe to ignore. Finally, you should fill in additional information about your genomes and annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. You can find them in the tool-data/ Galaxy directory. - History =======