Hi Kanwei, On Mon, Jan 31, 2011 at 5:16 PM, Peter <pe...@maubp.freeserve.co.uk> wrote: > On Wed, Jan 5, 2011 at 9:07 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: >> Hi Peter, >> >> We had some discussion today about Kanwei's email and opted for the >> nicer looking access method. I've added a note to the ToolConfigSyntax >> wiki page about special characters. >> >> Thanks, >> >> Dan > > Thanks Dan, > > Kanwei - could you merge/transplant this changeset to use the new > parameter settings in the NCBI BLAST+ wrappers please: > > https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 > > This is currently the only commit on this new branch, > > https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 > > This took a while because I wanted to get the other BLAST+ changes > merged first - and that's done now. > > Thanks, > > Peter
Actually there are two commits on that branch now, I've added a workaround for Galaxy issue 325 which is causing us real problems with BLAST warnings being treated as errors: https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c Once issue 325 is fixed, this wrapper script can be removed. Even my proposed first step of getting Galaxy to check the return code would allow a simpler workaround of redirecting stderr to stdout in the XML for the BLAST+ tools. Thanks, Peter _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
