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 Jackson<j...@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_plus/ncbi_blastn_wrapper.xml
https://bitbucket.org/galaxy/galaxy-dist/src/default/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
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
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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