David,
I think we should go with Peter's advice. I had seen a date of April 2011 in the distribution for the tools I examined, but he knows these tools very well, and I could have easily missed the July 2011 date. Loading from the Tool Shed is not difficult, but perhaps unnecessary.
So, for your purposes, starting simple is probably best. This would mean using what is in the distribution, i.e. the http://getgalaxy.org instructions.
I didn't cross post this reply to all of the lists to keep the Q & A on topic. However, I do encourage the developers to discuss this further on the galaxy-dev list, separate from your BLAST question, ideally in a brand new thread/subject line. If the wrappers should be updated (sounds like this is worth discussing) - maybe Peter or Ed can start up a new thread?
Thanks Peter for getting the most up-to-date information about these tools out to David & other galaxy-user readers,
And thanks David, you brought up a good topic, sounds like there might be some small tuning needed on the development side of things,
Take care,
Jen Galaxy team
On 2/10/12 3:19 AM, Peter Cock wrote:
On Thu, Feb 9, 2012 at 9:57 PM, Jennifer Jacksonjen@bx.psu.edu wrote:
Hi Peter,
It looks to me like there are versions both, with the Tool Shed version having the more recent date stamp. But if those extra functions are not needed, then yes, you are correct, the version included in the distribution would be enough.
Please send corrections if I have any of this wrong, so that David gets the best information,
Thanks Peter!
Jen
Hi Jen,
I'm not sure which date stamps you are looking at, since I think it is the other way round.
The NCBI BLAST+ wrappers shipped with Galaxy are currently at version 0.0.11, both in galaxy-central and galaxy-dist, dated 12 July 2011, e.g. here is the current XML file for the BLASTN wrapper:
https://bitbucket.org/galaxy/galaxy-central/src/default/tools/ncbi_blast_plu... https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/n...
Over on the Tool Shed, Edward Kirton has a forked copy of a much older version of these wrappers at v0.0.1. The push date of 7 Jun 2011 is probably from the toolshed migration, I believe the true date is well before that.
Edward added support for using local BLAST databases as a new Galaxy datatype, along with wrappers for makeblastdb and dustmasker. Assuming these have proved useful, it would make sense to merge these changes into the main BLAST+ wrappers.
I have CC'd the galaxy-dev mailing list (and Edward) which is probably a better place to discuss this than the galaxy-user list.
Peter