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.gruen...@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 > > Am 16.01.2015 um 08:22 schrieb Peter Cock: > > On Thu, Jan 15, 2015 at 6:57 PM, Ryan G <ngsbioinformat...@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/1422966f1ca88472b8685015f5a8cdd3dd0f1db9 > > ___________________________________________________________ > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > >
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