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NordicESMhub / galaxy-tools

Galaxy Tools maintained by NordicESMHub
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psy-maps tools fails on climate.usegalaxy.eu #27

Closed annefou closed 5 years ago

annefou commented 5 years ago

Traceback (most recent call last): File "/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/climate/psy_maps/db8d76da4174/psy_maps/psymap_simple.py", line 31, in import psyplot.project as psy # noqa: I202,E402 File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/site-packages/psyplot/init.py", line 7, in from psyplot.config.rcsetup import rcParams File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/site-packages/psyplot/config/init.py", line 18, in config_path = psyplot_fname() File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/site-packages/psyplot/config/rcsetup.py", line 921, in psyplot_fname configdir = get_configdir() File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/site-packages/psyplot/config/rcsetup.py", line 971, in get_configdir os.makedirs(p) File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/os.py", line 211, in makedirs makedirs(head, exist_ok=exist_ok) File "/usr/local/tools/_conda/envs/mulled-v1-bc2b1aa7b35a0e77adb619efefa50ceaeb3d54d77eac03581d98a78e6459b045/lib/python3.7/os.py", line 221, in makedirs mkdir(name, mode) OSError: [Errno 30] Read-only file system: '/opt/galaxy/.config'

annefou commented 5 years ago

The solution may be to re-define HOME environment variable in xml file e.g. HOME=pwd &&

bgruening commented 5 years ago

see https://github.com/galaxyproject/galaxy/pull/5193

Can you please add a profile (>= 18.01 ) to your tool, than it should work.

bgruening commented 5 years ago

I added it manually into the usegalaxy.eu tool, please try it again.

annefou commented 5 years ago

seems to be fixed. At least it works on climate galaxy.