Hi Stephen, Can you provide the error message from the job? You can look at bug-report for the the output dataset created by the data manager for the “Data Manager History (automatically created)” history in your saved histories. Also any other relevant information from the log would be great as well.
Thanks for using Galaxy, Dan On Jun 12, 2014, at 8:24 PM, Stephen E <sedwards...@hotmail.com> wrote: > I installed a local instance of galaxy approximately a month ago (build > 2014.04.14) and have since updated to latest_2014.06.02. It is running on > 64-bit Ubuntu 12.04. > > 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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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