search

usegalaxy-no / galaxyadmin

A repository for managing the work of the usegalaxy.no GalaxyAdmin team
0 stars 0 forks source link

Problems with the T-coffee tool #81

Open kjetilkl opened 1 year ago

kjetilkl commented 1 year ago

The T-coffee tool (in the Phylogenetics section) fails with errors which I suspect may be related to a badly written wrapper. There are updated versions of this tool that can be installed, and maybe that will magically fix the problems, but I don't have time to try it myself right now.

--ERROR:  : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE]
--ERROR:  : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE]

COULD NOT Append anything to /t_coffee.tmp/tmp.slurm.usegalaxy.no.29614///.29614.slurm.usegalaxy.no.error4tcoffee

--ERROR:  : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE]
--ERROR:  : Could Not Create Directory /t_coffee.tmp/ [FATAL:T-COFFEE]

COULD NOT Append anything to /t_coffee.tmp/tmp.slurm.usegalaxy.no.29618///.29618.slurm.usegalaxy.no.error4tcoffee
Traceback (most recent call last):
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee/t_coffee_to_cigar.py", line 47, in 
    main()
  File "/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/df6527887a18/t_coffee/t_coffee_to_cigar.py", line 30, in main
    with open(sys.argv[1]) as fh:
FileNotFoundError: [Errno 2] No such file or directory: 't_coffee_out.fasta_aln'