index building

[tickteng]

Hi,

I want to try this pipeline. I use udocker since I do not have the root privilege.
However, when I tried to build the index, I run the following command
createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml

I tweaked the createindex.cwl file by adding the --user-space-docker-cmd=udocker on the first line. However, when I run the command, I get no output, nor error, nor any progress notifications.
Am I running this correctly?
Any help would be appreciated.

[tickteng]

installed nodejs and it works now.

[yyoshiaki]

Keep it up!

[tickteng]

Hi again,
The index buildin was running smooth for a while.
It created the index for human, but when creating the index for virus, the following error appears.

INFO [job wget_virus] /tmp/me9s33oy$ udocker
--quiet
run
--volume=/tmp/me9s33oy:/XFkviA
--volume=/tmp/2q5gdjp4:/tmp
--workdir=/XFkviA
--rm
--env=TMPDIR=/tmp
--env=HOME=/XFkviA
alpine:3.9
wget
--output-document=viruses.fasta
https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/data/viruses.fasta 2> /tmp/me9s33oy/wget-stderr.log
INFO [job wget_virus] Max memory used: 13MiB
ERROR [job wget_virus] Job error:
("Error collecting output for parameter 'downloaded':\n../VIRTUS/tool/wget/wget.cwl:31:7: Did not find output file with glob pattern: '['viruses.fasta']'", {})
WARNING [job wget_virus] completed permanentFail
ERROR [step wget_virus] Output is missing expected field file:///home/virtus/VIRTUS/bin/createindex.cwl#createindex/wget_virus/downloaded
ERROR [step wget_virus] Output is missing expected field file:///home/virtus/VIRTUS/bin/createindex.cwl#createindex/wget_virus/stderr
WARNING [step wget_virus] completed permanentFail
INFO [workflow ] completed permanentFail
{
"downloaded_virus": null,
"starIndex_virus": null,
"starIndex_human": null,
"downloaded_genomefasta_human": null,
"salmon_index_human": null,
"downloaded": null
}
WARNING Final process status is permanentFail

[yyoshiaki]

in development v1.2.1, we fixed it. Can you try to switch the branch to development1.2.1 and re-try it?