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?