I've been trying to run the gdc-client tool to download a bam file into my workspace.
The docker image I'm using is docker.io/broadinstitute/gdc_downloader:1.0
The tool itself was downloaded from the GDC official website and is compatible with Linux.
When I try to run the tool in FireCloud I get the following error:
Process SyncManager-1:
Traceback (most recent call last):
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.process", line 258, in _bootstrap
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.process", line 114, in run
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.managers", line 550, in _run_server
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.managers", line 162, in init
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.connection", line 132, in init
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/multiprocessing.connection", line 256, in init
File "/home/cdompierre/gdc-client/bin/build/gdc-client/out00-PYZ.pyz/socket", line 224, in meth
error: AF_UNIX path too long
2018-05-15 18:24:10,346: ERROR: Unable to download 354b6d71-e11e-4867-8c47-b3f37e961be8:
If I pull the docker image and run it locally, the tool runs successfully and downloads the file. Also, this specific method has been run on FireCloud before without any issues.
It seems to me that there's some kind of problem opening a socket to the GDC server from within a FireCloud VM.
Has anyone seen anything similar?
Thanks in advance!