[galaxy-dev] May Galaxy News: GCCBOSC, Training Material Workshop, New pubs, jobs, ...

Hello all, The May 2018 Galactic News highlights what's going on in the Galaxy this month, including: - Lots of GCCBOSC 2018 news : - *Early registration ends May 11

Re: [galaxy-dev] extract extra info (logs) from history

Sounds like a good excuse to upgrade :) Sent from my iPhone > On 2. May 2018, at 16:40, Jochen Bick wrote: > > Thanks Devon, > > I think now I got it ;-). We are running 17.05 I might not have the "Summary > Options" ? I cannot find them... > > But maybe I can use

Re: [galaxy-dev] extract extra info (logs) from history

Thanks Devon, I think now I got it ;-). We are running 17.05 I might not have the "Summary Options" ? I cannot find them... But maybe I can use the flagstat tool for now. Cheers Jochen On 02.05.2018 16:34, Devon Ryan wrote: By default the logs are just to stdout. You need to use one of

Re: [galaxy-dev] extract extra info (logs) from history

By default the logs are just to stdout. You need to use one of the options (under "Summary Options" on the version on our instance) if you want things saved as a history item. Devon -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology

Re: [galaxy-dev] extract extra info (logs) from history

That's also an interesting tool. Which gives almost the same result as in the log file of at HISAT output. I'm not sure why the number of mapped reads are not 100% identical... but anyway can someone tell me, or maybe Devon did already, where is the log info of HISAT saved? Cheers Jochen

Re: [galaxy-dev] extract extra info (logs) from history

Flagstat might be a good choice here… Brad > On May 2, 2018, at 1:48 AM, Jochen Bick wrote: > > Hi Devon, > > do you mean Alignment Summary? How can I access that information and use it > for an other tool. > > Cheers Jochen > > > On 26.04.2018 14:14, Devon Ryan