Update SnpEff tools to capture important bug fix (download) and new sub-tools

[jennaj]

MTS: https://toolshed.g2.bx.psu.edu/view/iuc/snpeff/dd3622f501f3

Currently at .org:

SnpEff download v 4.3+T.galaxy1 (has the key bug)
SnpEff databases v 4.3+T.galaxy1
SnpEff eff v 4.3+T.galaxy1

Update:

• SnpEff download v 4.3+T.galaxy2

Add:

• SnpEff build v 4.3+T.galaxy3
• SnpEff chromosome info v @[email protected]

https://github.com/search?q=org%3Agalaxyproject+snpeff&type=Issues
https://github.com/search?q=org%3Agalaxyproject+snpeff&type=Commits

[jennaj]

All updated, no bug reports about them.

MTS most current versions are:

[jennaj]

Test for the biggest bug fix in here (closed out now): galaxyproject/tools-iuc#1354 (comment)

Short description: Tool wasn't retrieving the right database when it was nested. Now it does.

[wm75]

@jennaj the newly added chromosome-info subtool seems rather broken.

• With the Download on demand option it fails with a java.lang.RuntimeException: Cannot create directory '/cvmfs/main.galaxyproject.org/deps/_conda/pkgs/snpeff-4.3.1t-0/share/snpeff-4.3.1t-0/data/... error indicating that the tool tries to write outside the job working directory
• The Downloaded snpEff database in your history option fails to recognize suitable datasets - so you can't use it
• The locally installed snpEff database option I couldn't test on main because there doesn't seem to be any suitable database installed, but on the eu server this mode produces an OutOfMemoryy error

That leaves only the Custom ... option, which I don't have a test dataset for.

[jennaj]

Yo! Ok, those are problems. Didn't test everything (just that the requested nested snpeff genome was reportedly downloaded). Glad for the additional testing!

Want to open another ticket against the tool repo with this info? If could link it back, would be helpful.

Maybe the tools need more test cases, too?

I'll probably make a new "update when fixed" ticket for main here and reference this one. I can build some test history/cases up, including for Custom (is for output from using SnpEff build) and add to the ticket -- unless you do that first. Will look for a small genome with sufficient annotation available (source: GenBank), might actually have that already somewhere...

[wm75]

Opened galaxyproject/tools-iuc#2254. Yes, a PR should definitely also add more thorough tests.

[hepcat72]

These issues are pre-existing issues inherited from the snpeff eff tool. They didn't originate from the chromosome info tool. I'm not surprised they affect this tool as well. Neither of the history or custom options (which is also a history-related option) ever worked for me. I had rigged a way around it (galaxyproject/galaxy#6658) when I was trying to solve the issue during the development of the chromosome info wrapper when I was uploading a real snpeff database and selecting the snpeffdb data type. I submitted an issue for it too: galaxyproject/galaxy#6666. The problem is that the snpeff database type is not a real database. It's a 2 line text file that references an installed database that's used by a data handler. My jury-rigged solution (after uploading a real database) was to treat the history database as a real snpeff database when issuing the snpeff command. But once I realized that the history item wasn't supposed to be a real database, I removed my work-around solution. Ostensibly, the only way to create that metadata database history item is via the download tool which presumably installs the real database and creates the metadata file about it. But I could never get it to work.

See my comments #2254.

[wm75]

All the chromosome-info issues above and a related one with downloading a genome source on demand in snpEff eff have been addressed by @lparsons in galaxyproject/tools-iuc#2255. The tools have been updated in the MTS and on usegalaxy.eu and are working just fine now.

[jennaj]

Hi @wm75 -- I don't see updated tool revisions in the MTS but the repo update-date is newer now (1/25/19). EU server seems to be down so I can't compare against there right now.

What parts of the tool suite should we update from the MTS?

cc @davebx Re-opening this. Two things (at least) were changes to address issues. Might not have an updated tool version.

[wm75]

You are correct that the PR did not bump the versions of the affected tools (because of the clear bug-fix nature of the changes). The two tools with changes in the collection are SnpEff chromosome-info and SnpEff eff (or snpEff_get_chr_names and snpEff if you want tool ids), all others have remained untouched so just updating the collection should be fine.

[jennaj]

@davebx The tool version didn't change, so just lmk when the suite update is installed and I will test vs prior issues.

[davebx]

Updated to toolshed revision 8f92c2b26e6d on usegalaxy.org

[jennaj]

Thanks, testing

[jennaj]

Testing took longer than I expected, but am now convinced the tools are finally working correctly. Super!

Test history with most items (messy): https://usegalaxy.org:/u/jen/h/agamp3-snpeff-test

The "HTML stats" from toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 renders oddly but it might just need to be whitelisted, then we can close this out. ping @natefoo @martenson @davebx

[natefoo]

It looks like SnpEff eff version 4.3+T.galaxy1 is whitelisted and the latest HTML output in your test history looks ok to me? Closing this but feel free to reopen if it still seems broken.