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Support both HDFS and NFS/other file systems for BAM files

Open jaclynperrone opened this issue 10 years ago • 6 comments

for uploaded BAM files

jaclynperrone avatar Jul 20 '15 21:07 jaclynperrone

Cf. #682 #663

hammer avatar Jul 20 '15 21:07 hammer

I think it makes sense to support object stores (e.g. S3) as well for BAM/VCF storage.

hammer avatar Jul 20 '15 21:07 hammer

I'm testing out Cycledash as a way to compare test/truth VCFs, and to easily view discordant calls in IGV. Since our BAMs are not in HDFS, this issue seems to be the only bottleneck. Please advise on a workaround, if any. Thanks! And really nice work, so far.

ckandoth avatar Nov 25 '15 06:11 ckandoth

Thanks for checking out Cycledash, Cyriac! I'm looking into what's required on Cycledash's end to support this, and it looks like a relatively simple change that I hope to get to soon. On your side of things, the BAMs would need to be accessible via HTTP (using any old server that supports HTTP range requests—most HTTP servers barring Python's SimpleHTTPServer). Please let me know how else I can help, and I'll let you know when this feature is added.

ihodes avatar Nov 26 '15 07:11 ihodes

@ckandoth also you can sign up for our public Slack instance where we hope to support users of our software, some day: http://publicslack.hammerlab.org.

hammer avatar Nov 26 '15 07:11 hammer

Hi Cyriac; this should be fixed on #865 (not yet merged into master), so please feel free to give it a whirl if you'd like.

ihodes avatar Dec 17 '15 20:12 ihodes