I have split the RUN
up and isolated the issue down to this line:
RUN wget -O /miniconda/mtbdependencies/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 -U "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3029.110 Safari/537.36" chromium --referer https://software.broadinstitute.org/gatk/download/archive 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef'
The user agents and referral are to get around the way the website generates download URLs.
The code works fine on my ubuntu VM without the RUN
, but with RUN
in docker, it always returns error code 4. I cannot tell why because the download completes just fine:
2019-09-17 02:47:31 (1001 KB/s) - '/miniconda/mtbdependencies/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2' saved [14521011/14521011]
FINISHED --2019-09-17 02:47:31--
Total wall clock time: 16s
Downloaded: 1 files, 14M in 14s (1001 KB/s)
then the build stops and throws out this error.
There are previous wget
lines in the same dockerfile that did not cause this error.
Does anyone know what’s causing this?