deepvariant on ubuntu - httplib.ResponseNotReady about deepvariant

[pichuan]

Hi Tomasz,
this issue might be the same as an earlier one. See this comment for a temporary solution:
#7 (comment)

We are currently working on a fix, and will post an update to this github issue when it's fully fixed. Meanwhile, please let us know if you're having problems with the temporary fix.

[tstokowy]

Hi,
This temporary fixed worked out:

1. Set TF_NEED_GCP in settings.sh to 0
   export TF_NEED_GCP=0
2. Comment out line in make_examples.py and in call_variants.py
   "# htslib_gcp_oauth.init()"
3. build_and_test.sh works
4. I am able to run
   python-bazel-bin/deepvariant/make_examples --mode calling --ref ../input/ucsc.hg19.chr20.unittest.fasta --reads ../input/NA12878_S1.chr20.10_10p1mb.bam --regions "chr20:10,000,000-10,010,000" --examples ../output/output.examples.tfrecord

Thank you!

[depristo]

@tstokowy thanks for the pointer. We have a fix for this internally and it will arrive in the OSS version on our next push to the repo.

[scott7z]

This should be fixed in the most recent 0.4.1 binaries, and the HEAD of the r0.4 branch.