I can try a local toolshed, but the organization I work at frowns upon automatic installation for various reasons. That and it lets me see exactly how a tool is installed and works within my local instance. When a tool is installed from the toolshed, how does Galaxy know about it?
From a DB entry, or from the XML file(s) being present somewhere? I sort of like the idea of how /etc/profile.d gets scanned by /etc/bashrc when a user logs into a linux machine. This way, there is no modification of files, just placing the right files in the right directory is all that is needed. Anyway, I need to understand how Galaxy works with the toolshed.
On Fri, Jan 16, 2015 at 3:08 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
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
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
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
Am 16.01.2015 um 08:22 schrieb Peter Cock: the 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...
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