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msettles / expHTS

Python application for "Experimental High Throughput Sequencing"
Apache License 2.0
5 stars 3 forks source link

Explicit version checks and application version information #55

Open bricesarver opened 8 years ago

bricesarver commented 8 years ago

expHTS fails, with uninformative errors or no errors, when the 'incorrect' versions of called applications (sickle, scythe, etc.) are in $PATH. This can be handled efficiently by invoking submodules in git. Alternatively, at a bare minimum, the versions required should be listed.

msettles commented 8 years ago

Brice,

We had a call last Friday and we all agreed to let expHTS go defunct (partially at your suggestion) and start anew with the new sub applications David has created at are currently being tested and verified for correctness, the new app (post expHTS, yet unnamed) will use submodules to ensure versioning. AND include actual error output.

The new applications all support streaming of both SE and PE natively, most are ready to use, but David still needs to build a phiX screener and replacement for scythe (SE adapter detection), then all base apps are good to go and ready for a new pipeline handler.

Matt

From: Brice Sarver notifications@github.com Reply-To: msettles/expHTS reply@reply.github.com Date: Tuesday, May 31, 2016 at 10:40 AM To: msettles/expHTS expHTS@noreply.github.com Subject: [msettles/expHTS] Explicit version checks and application version information (#55)

expHTS fails, with uninformative errors or no errors, when the 'incorrect' versions of called applications (sickle, scythe, etc.) are in $PATH. This can be handled efficiently by invoking submodules in git. Alternatively, at a bare minimum, the versions required should be listed.

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bricesarver commented 8 years ago

Cool. I'm going to keep posting issues here so they can be addressed during the rewrite.

mfcovington commented 8 years ago

@msettles @dstreett Hey guys, I'd love to help out with the new app, its sub-apps, and/or building a docker image or biobox. Please let me know what currently needs the most assistance. Thanks.

msettles commented 8 years ago

That would be great Mike @mfcovington! So here is where things sort of stand, one thing you can really help out and is relevant to you I think is a nice robust RNAseq workflow. So where things stand right now and @samhunter and @dstreett should chime is David has rewritten all the primary apps to have a consistent look feel, native streaming (using tab-delimited) and can be mixed matched switched around as needed. The new apps are under David's repo https://github.com/dstreett?tab=repositories and primerNullifier, PruNe, FLASH2, Slasher, ATtack and we still need a PhiX screener and final stat generator. In theory you should be able to do something like

primerNullifier -t read1 read2 | FLASH2 -t -T - | Slasher -t -T - | PruNE -t -T - | ATtack -t

don't quote me on that as it was off the cuff, so whats needed is testing the apps finding the edge cases and such and if your interested we can add you to the next generation expHTS project to contribute some code? Hows that sound? Matt