1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/79236000c5bd/ changeset: 79236000c5bd user: greg date: 2012-03-21 21:53:26 summary: Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file. affected #: 2 files

diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 lib/galaxy/tool_shed/migrate/versions/0002_tools.py --- /dev/null +++ b/lib/galaxy/tool_shed/migrate/versions/0002_tools.py @@ -0,0 +1,17 @@ +""" +The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed from +datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The +repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +will be installed into your local Galaxy instance at the location discussed above by running the following command. + +vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv +sh ./scripts/migrate_tools/0002_tools.sh +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +""" + +import sys + +def upgrade(): + print __doc__ +def downgrade(): + pass

diff -r b1d33edc5dffc055867abefa7a666d0957eb0d00 -r 79236000c5bdceaf98546d66f002d5a40b006f74 scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /> - <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b"> + <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"><tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /><tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /><tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" />

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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