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,
Newer dependencies will likely next get an old fashioned package
on the Galaxy Tool Shed.
On Fri, Apr 7, 2017 at 12:18 AM, Bryan Hepworth
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.
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