Hi,
I am following this tutorial Running Jobs on Remote Resources with Pulsar step-13 and I have (at least) two problems:
1st problem:
When it comes to “Testing Pulsar” after I upload the data from Zenodo, I get this error when I try to run bwa-mem with it:
Could not display BAM file, error was:
file does not contain alignment data
Is it normal?
2nd problem:
On the VM where Galaxy is installed journalctl -fu pulsar displays -- Logs begin at Tue 2023-11-28 13:23:08 UTC. -- and stays there, whereas on the VM acting as Pulsar there is this error:
Nov 28 13:33:54 puluio pulsar[25370]: scheme, host, port, user, password, path, query = _parse_url(url)
Nov 28 13:33:54 puluio pulsar[25370]: File "/opt/uio/pulsar/venv/lib/python3.8/site-packages/kombu/utils/url.py", line 76, in url_to_parts
Nov 28 13:33:54 puluio pulsar[25370]: parts.port,
Nov 28 13:33:54 puluio pulsar[25370]: File "/usr/lib/python3.8/urllib/parse.py", line 185, in port
Nov 28 13:33:54 puluio pulsar[25370]: parts.port,
Nov 28 13:33:54 puluio pulsar[25370]: File "/usr/lib/python3.8/urllib/parse.py", line 185, in port
Nov 28 13:33:54 puluio pulsar[25370]: raise ValueError(message) from None
Nov 28 13:33:54 puluio pulsar[25370]: ValueError: Port could not be cast to integer value as 'oOnbWm8ejfMhwvB'
Nov 28 13:33:54 puluio pulsar[25370]: raise ValueError(message) from None
Nov 28 13:33:54 puluio pulsar[25370]: ValueError: Port could not be cast to integer value as 'oOnbWm8ejfMhwvB'
I tried with other tools and workflows, and they run on the Galaxy VM, as if there was no pulsar at all.
Any help to sort this out would be appreciated