Hi Kanwei, On Mon, Jan 31, 2011 at 5:16 PM, Peter <peter@maubp.freeserve.co.uk> wrote:
On Wed, Jan 5, 2011 at 9:07 PM, Daniel Blankenberg <dan@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