conda channel order in galaxy and planemo

[mvdbeek]

The channel order mechanism has changed between conda 3.19.3 (what we've been shipping galaxy with initially) and >= 4. The changes are documented here. This led us to notice that there are problems with the current order.

• currently planemo conda_install writes out a channel order that is wrong (i.e. different from bioconda). The current order is [defaults, conda-forge, r, bioconda, iuc] while it should be iuc, bioconda, r, defaults, conda-forge].

• need to verify that galaxy's channel order is correct

• looking up galaxy's channel order should be easy. log in galaxy log? log in tool run information ?

[bgruening]

Adding to the last point, the complete environment of a tool + channel order should be dumped as part of the metadata.

[nsoranzo]

while it should be [iuc, bioconda, defaults, r, conda-forge]

According to https://github.com/bioconda/bioconda-recipes/blob/master/config.yml , this should be:

[iuc, bioconda, r, defaults, conda-forge]

which is also what we already use in config/galaxy.ini.sample .

[mvdbeek]

updated the above -- I think that was a mistake when we we're working through some problems in gitter

[jmchilton]

Moved these logging issues to a new issue and closing this one.