Re: [galaxy-dev] git clone 16.10 bwa 0.7.15 data manager

[Peter Cock]

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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[galaxy-dev] git clone 16.10 bwa 0.7.15 data manager

[Bryan Hepworth]

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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