Mercurial > repos > gga > apollo_create_or_update

changeset 1:b194ffbd6ae1 draft

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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(-) [+]
line wrap: on
line diff
--- 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__