I'm having an issue with the Data Manager to fetch reference genomes (data_manager_fetch_genome_all_fasta, Rev. 2ebc856bce29). It will successfully submit a job to the queue but it quickly has an error. I'm selecting UCSC as the source and bosTau7 as UCSC's DBKEY for source FASTA.
The only error/warning I see in the server logs seems related to samtools:
galaxy.tools.deps DEBUG 2014-06-12 20:07:30,952 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps WARNING 2014-06-12 20:07:30,952 Failed to resolve dependency on 'samtools', ignoring
Samtools 0.1.19 seems to be installed through galaxy and I also installed samtools through apt-get. I installed the apt-get version after the first time trying this didn't work.
In the list of jobs, it has an error state and the command line is the following:
python /home/stephen/Work/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py "/home/stephen/Work/galaxy-dist/database/files/000/dataset_22.dat" --dbkey_description 'unspecified (?)'
I need to use the bosTau7 (or perhaps bosTau6) cow reference genomes and can't figure out any other ways to properly load them into galaxy. I'd like them available for everything on the server and would prefer this over using a custom reference genome. I may be missing something obvious because the command line doesn't seem to specify the genome I want but I can't type anything new into the "DBKEY to assign data" field.
How can I get the fetch genome data manager to work or otherwise load the bosTau7 reference genome into galaxy?
Thanks,
Stephen