Mercurial > repos > gga > apollo_create_or_update
changeset 1:b194ffbd6ae1 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
| author | gga |
|---|---|
| date | Tue, 19 Sep 2017 12:22:46 -0400 |
| parents | cd595b5d890a |
| children | aac9ef1f72e7 |
| files | README.rst create_or_update_organism.xml |
| diffstat | 2 files changed, 18 insertions(+), 5 deletions(-) [+] |
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--- a/README.rst Mon Sep 11 05:46:00 2017 -0400 +++ b/README.rst Tue Sep 19 12:22:46 2017 -0400 @@ -6,7 +6,20 @@ available <https://github.com/galaxy-genome-annotation/python-apollo>`__ as a pip-installable package. -Environ +Dependencies +------------ + +You will need to install some python modules in the Galaxy virtualenv for these +tools to be fully functional: + +.. code:: bash + + . /path/to/galaxy/.venv/bin/activate + pip install future biopython bcbio-gff + deactivate + +Environment +----------- The following environment variables must be set: @@ -24,9 +37,9 @@ | | | | | | +--------------------------------+-----------------------------------------------------------+ -| ``$GALAXY_WEBAPOLLO_EXT_URL`` | users. May be relative or absolute. | +| ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. | | | The external URL at which Apollo is accessible to end | -| | | +| | users. | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to | | | exchange JBrowse instances. |
--- a/create_or_update_organism.xml Mon Sep 11 05:46:00 2017 -0400 +++ b/create_or_update_organism.xml Tue Sep 19 12:22:46 2017 -0400 @@ -7,7 +7,7 @@ <expand macro="requirements"/> <code file="webapollo.py"/> <command detect_errors="aggressive"><![CDATA[ -cp -R '${jbrowse.extra_files_path}/data/' '@DATA_DIR@/${jbrowse.id}' +cp -R '${jbrowse.extra_files_path}/data/' "@DATA_DIR@/${jbrowse.id}" && @@ -25,7 +25,7 @@ @ORG_OR_GUESS@ -'@DATA_DIR@/${jbrowse.id}' +"@DATA_DIR@/${jbrowse.id}" $__user_email__