Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Looks like I’m hitting this issue: https://github.com/galaxyproject/galaxy/issues/2797 Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy > On 29 Aug 2016, at 11:09 AM, Steve Cassidy wrote: > > Thanks Marius, > I tried a

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Hi Steve, Looks like you're running an older version of galaxy in the docker container, since newer galaxy will build the metadata environment in a separate environment called 'conda-metadata-env', and we have also changed the way that the handlers receive their Python environment (that's why

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Nah, definitely baby steps… so, in the repo you point to there seems to be an error in the Dockerfile, the ENV line should use the var=value syntax to have more than one setting on one line (maybe that’s changed recently in docker). with this I built a new docker image, when I run my first

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Hi Steve, you call this baby-steps? I think this is huge! :) All what you are missing is to enable conda in Galaxy. Look at Gregs new flavour which is entirely Conda/Galaxy based. You need to enable these env vars to make Galaxy conda enabled:

[galaxy-dev] Putting it all together - toolshed tool + conda dependency

Hi all, I’m making baby steps towards having a repeatable installation for my tools. But I’m now stuck, so help would be appreciated. I have a tool that works and is in the test toolshed (alveoimport in Data Sources). It depends on my python package which is now part of bioconda (pyalveo,