Hi Ryan,
what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own.
Cheers, Bjoern
Am 16.01.2015 um 08:22 schrieb Peter Cock:
On Thu, Jan 15, 2015 at 6:57 PM, Ryan G ngsbioinformatics@gmail.com wrote:
Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes.
Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool.
So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct.
Ryan
The old pre-ToolShed way to add a new datatype was indeed to add it to datatypes_conf.xml and put any Python file into the galaxy-dist/lib/galaxy/datatypes/
I'm still doing this on some of my locally developed tools, but now they are in the ToolShed perhaps I should switch to using that...
Regards,
Peter
P.S. You also used to need to add an import line to the galaxy-dist/lib/galaxy/datatypes/registry.py but that is not longer required as of this bug fix: https://bitbucket.org/galaxy/galaxy-central/commits/1422966f1ca88472b8685015... ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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