Update BEDtools to version 2.27.1 (new in MTS)

[jennaj]

Version 2.27.1 (and 2.27.2 for "Map Bed") of the tools incorporate many important bug fixes and tool form improvements.

Example of a problem resolved with new tool form options: Intersect BED will always fail with two BAM inputs in the currently installed version 2.27.0.2. An option to output bed output was added in the update and avoids errors that end with a "bug report" message similar to ***** ERROR: writeAllOverlap option is not valid with BAM query input unless bed output is specified with -bed option. *****

Workaround for end-users: Use coordinate sorted bed inputs instead (tool: BAM to BED). Or, use bam inputs with the tool(s) at https://usegalaxy.eu if you are experiencing errors at https://usegalaxy.org until this issue is closed out and the updated tools are added to https://usegalaxy.org. At the EU server, double check the top of the tool form to make sure that version 2.27.1 or later is being used and switch to the latest version as needed using the "Versions" menu at the top of the tool form -- an earlier version of the tool may load by default when loading a form from the left panel. If your job errors for a resource related reason (memory or walltime/runtime), the inputs could really be too large or you might need to sort your inputs (e.g. coordinate sort: chrom + start coordinate).

MTS: https://toolshed.g2.bx.psu.edu/view/iuc/bedtools/87ee588b3d45

• Test history ORG: https://usegalaxy.org:/u/jen/h/test2-bedtools-intersectbed
• Test history EU: https://usegalaxy.eu:/u/jenj/h/test-bam-intersect works with 2 bam inputs

ORG bam dataset 26 == EU bam dataset 1
ORG bam dataset 28 == EU bam dataset 2

Tickets/PRs related to the update are numerous, toogle closed/open to review those incorporated in the latest release and pending to-do items: https://github.com/search?q=org%3Agalaxyproject+bedtools&type=Issues

[jennaj]

Status -- Rerunning EU test, Main not updated yet

[jennaj]

EU test completed -- updated tool version accepts 2 bam inputs. Updating tool on main should resolve the issue there.

[jennaj]

@qiagu I cannot assign this ticket to you. Please check with @natefoo or @martenson to determine why & resolve. Then you can assign yourself :)

[qiagu]

@jennaj well, we've already discussed on slack. I probably can't solve this issue without admin privilege to usegalaxy.org, which I don't think I have right now.

[jennaj]

@qiagu Pretty sure that is unrelated. Let's bring the chat back internally again and figure it out :)

[davebx]

I was able to give @qiagu admin access last week, so that's no longer a blocker.

[jennaj]

Status? @qiagu @davebx

[qiagu]

@davebx Actually, the blocker is still there.

[davebx]

I've updated bedtools myself, pending ssh access for @qiagu.

[jennaj]

Missing dependencies -- @natefoo fixing

Additional test history: https://usegalaxy.org:/u/jen/h/test-bedtools-multicovbed