comparison readme.rst @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

5:84584664264c

Read more about the "Phone Home" problem at:
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

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
=======

* v0.1      - Initial public release

6:35c00763cb5c

Read more about the "Phone Home" problem at:
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

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
=======

* v0.1      - Initial public release