Example workflow `fetchngs` fails on fresh install

[neoformit]

I have installed Cloudgene on a VM behind Nginx.
I have followed the setup docs, but the example workflow fails with the error below.

Ubuntu 24.04 LTS
Java 17
Nextflow version 25.04.6.5954

job.txt:

25/08/07 01:44:03 Setup External Workspace on Local Workspace
25/08/07 01:44:03 Details:
25/08/07 01:44:03   Name: TEST
25/08/07 01:44:03   Job-Id: job-20250807-014403-279
25/08/07 01:44:03   Submitted On: Thu Aug 07 01:44:03 UTC 2025
25/08/07 01:44:03   Submitted By: admin
25/08/07 01:44:03   User-Agent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/138.0.0.0 Safari/537.36
25/08/07 01:44:03   Inputs:
25/08/07 01:44:03     IDs: /mnt/data/cloudgene/workspace/job-20250807-014403-279/input/input/upload_1590681840088045766ids.csv
25/08/07 01:44:03   Outputs:
25/08/07 01:44:03     Output: /mnt/data/cloudgene/workspace/job-20250807-014403-279/outdir
25/08/07 01:44:03 Executing Job....
25/08/07 01:44:03 Planner: WDL evaluated.
25/08/07 01:44:03 Execute 1 steps...
25/08/07 01:44:03 ------------------------------------------------------
25/08/07 01:44:03 Fetch Data
25/08/07 01:44:03 ------------------------------------------------------
25/08/07 01:44:03 Warning: Nextflow script '/mnt/data/cloudgene/apps/fetchngs/1.12.0/nf-core/fetchngs' not found. Try to resolve it on github as 'nf-core/fetchngs'
25/08/07 01:44:03 Wrote params to file '/mnt/data/cloudgene/workspace/job-20250807-014403-279/step1-params.json'
25/08/07 01:44:03 Command: [/bin/bash, -c, PATH=$PATH:/usr/local/bin /usr/local/bin/nextflow -log /mnt/data/cloudgene/workspace/job-20250807-014403-279/logs/step1-nextflow.log run nf-core/fetchngs -r 1.12.0 -w /mnt/data/cloudgene/workspace/job-20250807-014403-279/temp/nextflow -params-file /mnt/data/cloudgene/workspace/job-20250807-014403-279/step1-params.json -ansi-log false -with-weblog http://localhost:8082/api/v2/collect/0594eaf7d7562eac79ec3b6a2bcad8fb2ea7ce59323fd1cc1ff327a85abe8032 -with-trace /mnt/data/cloudgene/workspace/job-20250807-014403-279/logs/step1-trace.csv -with-report /mnt/data/cloudgene/workspace/job-20250807-014403-279/logs/step1-report.html -with-timeline /mnt/data/cloudgene/workspace/job-20250807-014403-279/logs/step1-timeline.html]
25/08/07 01:44:03 Working Directory: /mnt/data/cloudgene/workspace/job-20250807-014403-279
25/08/07 01:44:03 Exit Code: 1
25/08/07 01:44:03   Fetch Data [ERROR]
25/08/07 01:44:03 Job Execution failed: Job Execution failed.
25/08/07 01:44:03 Cleaning up...
25/08/07 01:44:03   Exporting parameter outdir...
25/08/07 01:44:03 Cleanup successful.


std.out:

mkdir: cannot create directory �/var/www/.nextflow/tmp�: Read-only file system
mkdir: cannot create directory �/var/www/.nextflow/framework�: Read-only file system

I checked the /mnt/data/cloudgene/apps/fetchngs/1.12.0/ folder and it seems like it has failed to download the target workflow, even though https://github.com/nf-core/fetchngs exists:

~/cloudgene/apps/fetchngs/1.12.0$ l -a
total 20K
drwxr-xr-x 2 www-data www-data 4.0K Aug  7 01:41 .
drwxr-xr-x 3 www-data www-data 4.0K Aug  7 00:23 ..
-rw-r--r-- 1 www-data www-data  653 Jul  9  2024 cloudgene.yaml
-rw-r--r-- 1 www-data www-data 1.1K Jul  9  2024 LICENSE
-rw-r--r-- 1 www-data www-data   57 Jul  9  2024 README.md

[neoformit]

FYI I think this was actually a silent permission error - running Cloudgene as a different user seemed to fixed this