Hi Bryan,
I suspect the missing dependency BWA may reflect the switch away
from Galaxy's home-grown packaging system to using Conda -
enabled by default since v17.01,
https://docs.galaxyproject.org/en/master/admin/conda_faq.html
Newer dependencies will likely next get an old fashioned package
on the Galaxy Tool Shed.
Peter
On Fri, Apr 7, 2017 at 12:18 AM, Bryan Hepworth
wrote:
> Hi All
>
> I've been trying to get a local galaxy running with an assortment of tools
> for a local researcher. I'm a linux administrator rather than a
> bioinformatics researcher and am familiar with how repo's work for RedHat, R
> and the like. I've built tools for other groups at work and from my reading
> it looked like galaxy was working on similar lines for keeping things in step.
>
> I've done a git clone of 16.10 into /galaxy altered the galaxy.ini to
> postgresql and added me as admin. Done the sh run.sh to get a feel for how
> everything goes together. I've pulled reference genomes from the source and
> have had some success converting to different formats. I bumped up against a
> few dependency issues so I've also enabled the test repo.
>
> The first stumbling block on the most recent build is getting bwa on there
> with the data manager route - it has a dependency on bwa 0.7.15, but try as I
> might I don't seem to be able to find an instance of package_bwa_0.7.15
> anywhere on the devteam repo's to get over this hurdle. I'm guessing I'm
> missing something really simple as it isn't pulling in dependancies as the
> documentation suggests it should. I'd be really grateful for any pointers.
>
> Bryan
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