<version_command>block so there's no way to tell whether updating should be done or not (depends on user settings).
which might update its environment as part of its <command> section
The conda env? That sounds wrong to me.
utils\localization.jsfile in 100+ of our VUE & JS Galaxy files? Is this necessary since there are only 3 files in the codebase where language can be changed by the user? (e.g. Home Page, Login Page, and Preferences Page)
@bgruening:matrix.org for the particular usecase I was wondering if the ncbi taxonomy data table could be reused.
manual merge and deploy? if this happens more often it would be cool to have a way to disable size checks for certain paths .. maybe an additional file like
on the long run progress with galaxyproject/galaxy#13495 :)
was just wondering if we could use the data on the CVMFS for this case (use cached in the tool's conditional). But its kind of circular, since we would need the data manager or at least the datatable + data on CVMFS before accepting the tool. Also CI would need to be adapted to set the
--tool_data_table parameter of
Just checked recent weekly CI errors. Seems that
samtools sort output may depend on the number of used CPUs (sorting is correct, just the order of alignments with the same mapping position may differ). Wondering how to deal with this ..
Just check for the number of lines and maybe some regex (does this work for bam?)?
mapper | samtools sort -@2 ... | samtools -@\$GALAXY_SLOTS.. which also solves the problem the parallel sorting and mapping may use to many CPUs
I was trying to figure out why most of the tool tests of all versions of Pangolin 3.x fail on usegalaxy.org with:
AttributeError in line 112 of /usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk: 'DecisionTreeClassifier' object has no attribute 'n_features_' File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk", line 112, in __rule_pangolearn File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/pangolearn/pangolearn.py", line 170, in assign_lineage File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 922, in predict_proba File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 395, in _validate_X_predict File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/concurrent/futures/thread.py", line 57, in run Exiting because a job execution failed. Look above for error message
Both conda and singularity, and so wanted to see how usegalaxy.eu had fixed it - turns out, it's broken on EU too.
Error: the input query fasta could not be parsed. Double check your query fasta and that compressed stdin was not passed. Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions. Error: the input query fasta could not be parsed. Double check your query fasta and that compressed stdin was not passed. Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions. rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/out.3651279': No such file or directory rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/err.3651279': No such file or directory