I believe shipping a mapping file with Galaxy (& galaxy-lib) is a good
way to go - there is an existing github issue on this:
Hopefully this could be made generic enough to be useful with other
resolvers such as environment modules and future resolvers such as
On Sun, Jul 3, 2016 at 4:52 PM, Peter van Heusden <p...@sanbi.ac.za> wrote:
> Hi there
> I'm trying to satisfy requirements on our RNA-seq oriented Galaxy server at
> SANBI using conda/bioconda. There's a disconnect between the names used in
> tool dependency tags and the names of conda recipes though, for example:
> 1) the BAM to BigWig converter (tool ID CONVERTER_bam_to_bigwig_0) has a
> requirement for ucsc_tools. The tool it needs, bedGraphToBigWig, is provided
> by the ucsc-bedgraphtobigwig package, so in this case ucsc_tools is a
> broader requirement than what bioconda provides.
> 2) the featurecounts tool requires featurecounts, which is part of the
> subreads recipe, so in this case featurecounts is a narrow requirement than
> what is provided in bioconda.
> In the second case, one could say subreads provides the featurecounts
> requirement. In the first case one could say the tool requires a narrower
> requirement than what it specifies, although the bioconda recipes split a
> single upstream package (ucsc_tools) into multiple recipes that invariable
> will be updated together, a somewhat strange choice.
> Right now I'm resolving these problems by manually creating environments
> (e.g. __package__featurecounts@__unversioned__) that will get picked up by
> the conda dependency resolver, but I'd like to hear from the list what the
> best way to support this is? Probably the easiest is keeping the tool
> requirements definition in line with what the conda recipe is called, but in
> some cases a mapping table between requirements and conda recipe names could
> be useful.
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