comparison tomo/test.txt @ 83:9b6e931e0de0 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty

83:9b6e931e0de0

I had a Galaxy tool crash repeatedly on Friday and tried a bunch of things, but nothing helped. Today I tried it from scratch and kept notes:

Removed everything in:
 /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess
and in:
/nfs/chess/galaxy-dev/var/dependencies/_conda/envs

Rebooted the ansible

Made sure that the repo in the testtoolshed is up to date.

Reinstall the CHAP tool at:
https://galaxy-dev.classe.cornell.edu/admin/toolshed
Watching its progress, I can see that it first clones the tool repo and then installs the tool dependencies.
When done, I have the following new content in the galaxy tree:
ls -al /nfs/chess/galaxy-dev/var/dependencies/_conda/envs:
drwxr-xr-x 3 galaxy galaxy 32 May  1 09:17 .
drwxr-xr-x 5 galaxy galaxy 52 Apr 28 08:40 ..
drwxr-xr-x 3 galaxy galaxy 26 May  1 09:18 chap_test_20230411

ls -al /nfs/chess/galaxy-dev/var/shed_tools/testtoolshed.g2.bx.psu.edu/repos/ximgchess:
drwxr-xr-x  6 galaxy galaxy  317 May  1 10:04 .
drwxr-xr-x 15 galaxy galaxy  226 Aug 29  2021 ..
drwxr-xr-x 12 galaxy galaxy  184 May  1 10:03 __ChessAnalysisPipeline@0.0.2
-rw-r--r--  1 galaxy galaxy    0 May  1 09:18 .conda_envs_dir_test
drwxr-xr-x 27 galaxy galaxy 4096 May  1 10:02 mulled-v1-0cd3a5ccc731743d38833d0396752d8219d106c20bb3bb478c34e74608ecb1c3
drwxr-xr-x 26 galaxy galaxy 4096 May  1 09:51 mulled-v1-67ac3841866ce74ad34393f2abb6cc61f6651a9d3f3e677b9821c88c9b0a676e
drwxr-xr-x 12 galaxy galaxy  184 May  1 10:04 mulled-v1-b1085bc9e4a5d280004f5b197e8295b3ef5167ea9ea22a074defb863f1b86458

When running a Galaxy tool and only when I try to pip install certif-pyspec, it bombs with:
OSError: [Errno 30] Read-only file system: '__config__.cpython-310.pyc'

See stdout and stderr in:
/nfs/chess/aux/reduced_data/user/galaxy-dev/jobs/002/2440/outputs