Runtime issues while using docker image

[tushu1232]

Trying to run but come across the following error

docker run -it -v $PWD/input:/dv2/input -v $PWD/models:/dv2/models \

gcr.io/deepvariant-docker/deepvariant:$IMAGE_VERSION

Unable to find image 'gcr.io/deepvariant-docker/deepvariant:0.4.0' locally
0.4.0: Pulling from deepvariant-docker/deepvariant
Digest: sha256:72d3bd936dfbfbb707e648d7e6f0f8fb4318eb115aad0bfde9b43ff05fef8f19
Status: Downloaded newer image for gcr.io/deepvariant-docker/deepvariant:0.4.0
root@720aed86585e:/#
root@720aed86585e:/# ./opt/deepvariant/bin/make_examples \

--mode calling \
--ref /dv2/input/ucsc.hg19.chr20.unittest.fasta.gz \
--reads /dv2/input/NA12878_S1.chr20.10_10p1mb.bam \
--examples output.examples.tfrecord \
--regions "chr20:10,000,000-10,010,000"

Traceback (most recent call last):
File "/tmp/Bazel.runfiles_PMLPk5/runfiles/genomics/deepvariant/make_examples.py", line 1015, in
tf.app.run()
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/platform/app.py", line 48, in run
_sys.exit(main(_sys.argv[:1] + flags_passthrough))
File "/tmp/Bazel.runfiles_PMLPk5/runfiles/genomics/deepvariant/make_examples.py", line 966, in main
htslib_gcp_oauth.init()
File "/tmp/Bazel.runfiles_PMLPk5/runfiles/genomics/deepvariant/core/htslib_gcp_oauth.py", line 79, in init
token = cloud_utils.oauth2_token()
File "/tmp/Bazel.runfiles_PMLPk5/runfiles/genomics/deepvariant/core/cloud_utils.py", line 58, in oauth2_token
credentials = oauth2_client.GoogleCredentials.get_application_default()
File "/usr/local/lib/python2.7/dist-packages/oauth2client/client.py", line 1271, in get_application_default
return GoogleCredentials._get_implicit_credentials()
File "/usr/local/lib/python2.7/dist-packages/oauth2client/client.py", line 1256, in _get_implicit_credentials
credentials = checker()
File "/usr/local/lib/python2.7/dist-packages/oauth2client/client.py", line 1187, in _implicit_credentials_from_gce
if not _in_gce_environment():
File "/usr/local/lib/python2.7/dist-packages/oauth2client/client.py", line 1042, in _in_gce_environment
if NO_GCE_CHECK != 'True' and _detect_gce_environment():
File "/usr/local/lib/python2.7/dist-packages/oauth2client/client.py", line 999, in _detect_gce_environment
http, _GCE_METADATA_URI, headers=_GCE_HEADERS)
File "/usr/local/lib/python2.7/dist-packages/oauth2client/transport.py", line 282, in request
connection_type=connection_type)
File "/usr/local/lib/python2.7/dist-packages/httplib2/init.py", line 1659, in request
(response, content) = self._request(conn, authority, uri, request_uri, method, body, headers, redirections, cachekey)
File "/usr/local/lib/python2.7/dist-packages/httplib2/init.py", line 1399, in _request
(response, content) = self._conn_request(conn, request_uri, method, body, headers)
File "/usr/local/lib/python2.7/dist-packages/httplib2/init.py", line 1355, in _conn_request
response = conn.getresponse()
File "/usr/lib/python2.7/httplib.py", line 1123, in getresponse
raise ResponseNotReady()
httplib.ResponseNotReady
root@720aed86585e:/#

[depristo]

We are pretty certain this is due to the same bug noted in #7. We have a fix already internally and will make it available as soon as possible. In the meantime, if you need this to work you can follow the same trick of commenting out the call to token = cloud_utils.oauth2_token() and replacing it with token = None. Sorry about that.

[rpoplin]

We believe this should be fixed now in the 0.4.1 docker image.

IMAGE_VERSION=0.4.1
gcloud docker -- pull gcr.io/deepvariant-docker/deepvariant:$IMAGE_VERSION
docker run -it -v $PWD/input:/dv2/input -v $PWD/models:/dv2/models \
    gcr.io/deepvariant-docker/deepvariant:$IMAGE_VERSION

Cheers,