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?