Hi Liisa and Peter, There was an issue if your workflows were created using the ncbi blast tools from the distribution (e.g. versions 0.0.11) and you only had installed the latest tools from the toolshed (e.g. versions 0.0.13). This has been corrected in changesets 7754:371f6770d25c through 7756:c76e2882d2d2 and will be available in the next distribution. Please let us know if you are still experiencing issues after the update us released.
The preferred method for handling tools that have been migrated is to use the provided migration scripts (in this case ' sh ./scripts/migrate_tools/0004_tools.sh' or 'sh ./scripts/migrate_tools/0004_tools.sh install_dependencies') and then starting the Galaxy server; after running the migrations to get the original tool versions installed, you can then install the the newest versions of the tools via the admin interface. However, using the migration scripts is optional, and you can always install the original tools via the admin interface, or manually, if that is desired. Thanks for using Galaxy, Dan On Sep 26, 2012, at 9:29 AM, Peter Cock wrote: > On Wed, Sep 26, 2012 at 2:20 PM, Liisa Koski <liisa.ko...@basf.com> wrote: >> Thanks Peter, >> It was in fact the snffier type. I changed it to <sniffer >> type="galaxy.datatypes.blast:BlastXml"/> > > And its all working now (as far as you can tell)? > >> I am using the July07 distribution. The reason I installed the datatypes >> manually is because when I did it via the directions with the toolshed all >> my workflows that used blast tools were broken. They could no longer find >> the blast tools. So I immediately removed the toolshed installation and >> tried to set up as before. With the blast wrappers back in the >> tools/ncbi_blast_plus directory. Now my workflows are functional again. > > That is strange - and one for the Galaxy team to puzzle over. > I've not tried this myself (since I'm actively developing the > BLAST+ wrappers, and often trying things before pushing > them to the ToolShed for wider user, it is easier for me to > install them locally via the manual route). > > Thanks for your feedback, > > Peter > ___________________________________________________________ > 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/ ___________________________________________________________ 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/