data_manager_fetch_genome_dbkeys_all_fasta can run multiple times for the same dbkey [was: BMW-MEM datamanager creating multiple symlinks to a file]

galaxyproject / tools-iuc

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data_manager_fetch_genome_dbkeys_all_fasta can run multiple times for the same dbkey [was: BMW-MEM datamanager creating multiple symlinks to a file] #2673

Open afgane opened 5 years ago

afgane commented 5 years ago

Running BWA-MEM datamanager tool, seeing the following output:

$ ls -l dataset_133_files/
total 4
lrwxrwxrwx 1 galaxy galaxy 116 Nov  9 13:33 sacCer2.fa -> /cvmfs/data.galaxyproject.org/byhand/sacCer2/seq/sacCer2.fa,/galaxy/server/database/tool-data/sacCer2/seq/sacCer2.fa
$ head dataset_133_files/sacCer2.fa 
head: cannot open 'dataset_133_files/sacCer2.fa' for reading: No such file or directory

It seems all the fasta files with the same name are being discovered and symlinked?

mvdbeek commented 4 years ago

That's when a data manager has been run twice (in this case not bwa-mem but the data manager that produces fasta files, probably data_manager_fetch_genome_dbkeys_all_fasta), this needs to be manually fixed (the symlinks shouldn't even be needed), and we can probably have some logic that prevents running a data manager twice.