clean environments

[matthdsm]

xref #340

• move atropos from python3 > default env
• move bismark from python2 > default env (no python dependencies), remove subversion pin
• move gemini to default env
• move cpat to default env
• move crossmap to default env, no longer uses pysam pi
• remove bedtools version pin
• remove bamtools version pin
• remove eriscript env
• remove freebayes version pin
• move gvcf-regions to default env since recipe is "noarch"
• move hisat2 to default env
• move lumpy-sv to default env, conda pkgs is noarch
• move macs2 to default env
• move manta to default env
• bump mirdeep version
• move peddy to default env
• move smoove to default env
• move vawk to default env

feel free to edit/comment

Cheers M

[naumenko-sa]

Thanks @matthdsm! Such cleaning makes a lot of sense!

We are pushing now for R3.5.1 > R3.6 change, which is a more pressing priority. once we are done, we'll return to this PR.

After some discussions we think that

• removing python3 env and moving the packages to default python3 would be the easiest thing.
• then we should be more careful with unpinning, as each pin probably was a result of a painful debug. We should not unpin them altogether to avoid a chain reaction of mutual incompatibilities, but do one by one and test for typical use cases.