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  • Oct 14 2017 11:03
    bmpvieira unassigned #16
  • Jun 02 2017 13:52
    bmpvieira commented #16
  • Jun 02 2017 13:44
    thejmazz commented #16
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    Create CODE_OF_CONDUCT.md addr… Merge pull request #15 from aya… (compare)

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Julian Mazzitelli
@thejmazz
At some point I'll go through the old private chat and bring out important points/links that I think should be here. A public chat is better b/c we can now collaborate with others much simpler!
Julian Mazzitelli
@thejmazz
Whitepaper on Nextflow + Docker + Univa Grid Engine on cluster: http://www.nextflow.io/misc/Univa-Docker-Whitepaper_FINAL.pdf
Julian Mazzitelli
@thejmazz
Julian Mazzitelli
@thejmazz
@/all draft post on NGS workflows: bash, make, snakemake, nextflow, bionode proposal https://github.com/thejmazz/jmazz.me/blob/master/content/post/ngs-workflow.md
Max Ogden
@maxogden
@thejmazz can you link me to the hangout?
@thejmazz i have https://plus.google.com/events/clroo9s4r4tqvj49v1bco7aebd8 but it wotn let me join
Julian Mazzitelli
@thejmazz
sec, yeah I cant start it b/c bionode@bionode.io needs to have hangouts enabled from google apps admin
so Im making my own right now
or someone call volunteer to screen record lol
Max Ogden
@maxogden
ok we can use https://bit.ly/datchat if you want
oh you wanna record it, gotcha
ya just make your own then
Julian Mazzitelli
@thejmazz
yeah, we have meet.bionode.io already for misc non recorded chats lol
Max Ogden
@maxogden
can you linkme to the actual hangout
i cant join from that page
@thejmazz i think you have to open the hangout page and link the url from the popup window
Julian Mazzitelli
@thejmazz
true
I also invited to email
Julian Mazzitelli
@thejmazz
where do I go to see the video now loll..
Julian Mazzitelli
@thejmazz
Hey I got a first basic pipeline with somewhat of the proposed api working. It's blocking, so does sra download, then uses globby based on provided output pattern to call fastq-dump with proper param
Im going home now but gonna work more tonight
For handling steams for this cat sra | fastq-dump, I think there are 2 ways to go:
Have ncbi.downloadStream(db, accession) which wont give progress but the actual http stream (could also be a search and then fetch I just realized) OR
check fs for files matching the pattern either on a repeat timeout or on first .on('data') or .on('start'),and then make an fs.createReadStream to pipe that to stdin for fastq-dump