Hi Laura This needs to be configured for your site. You will need the databases to be searched set up locally and you may need to edit the Artemis scripts that run blast. There is some documentation in the manual for Configuring the Run Menu¹.
The error you get may mean that blastall is not in your PATH. If you are using blast+ you will need to change the script to use legacy_blast.pl. You can test the script from the command line and this is a way of debugging it: etc/run_blastp file_of_filenames database The other option is to use the Run->NCBI searches option. Regards Tim On 8/17/11 8:04 PM, "Laura Lorenz" <lalore...@gmail.com> wrote: > I am trying to run batch blasts on a genome in Artemis but recieve an error > whenever trying to run blast (particularly blastp) from within Artemis. The > error is > > nice:invalid option -- 'd' > Try 'nice --help' for more information > > I assume this means the command after nice ($EXEC) is not specified properly. > How do I fix this? > > Thank you, > Laura > > > _______________________________________________ > Artemis-users mailing list > Artemisfirstname.lastname@example.org > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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