Peter, this is great and we will look at it. The main thing I want to
think about is does this affect reproducibility in any way. We may
want to keep the old tool, and have another tool for the NCBI version
(I'd love to see a complete set of wrappers for NCBI blast+, which we
could include with our cloud images right away). Thanks!
Department of Biology
Department of Mathematics & Computer Science
On Sep 21, 2010, at 11:12 AM, Peter wrote:
On Tue, Sep 21, 2010 at 2:13 PM, Peter
> I have a query about the existing Megablast wrapper, Python code
> Looking at the above, it is clearly trying to call the command line
> 'megablast' which is part of the NCBI 'legacy' BLAST suite. This is
> replaced by the command line tool 'blastn' in the new NCBI BLAST+
> suite (the default 'task' parameter is megablast).
> Currently the wiki instructions appear to be wrong, quoting:
>>> Megablast installation
>>> Megablast is a part of the BLAST+ suite of tools. To download it,
>>> go to the
>>> Megablast page and go to the download link. Select the BLAST+ file
>>> appropriate to your platform, noting that Galaxy uses version
>>> 2.2.22 currently.
>>> There is some information about installation in the BLAST+ user
>>> available from the download page.
> Quoted from http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup
> Have I misunderstood? Perhaps the script expects the be able to call
> 'megablast' via legacy_blast.pl - but most likely the documentation
> out of sync any the Galaxy servers have both BLAST and BLAST+
> I think it would make sense to update megablast_wrapper.py to call
> BLAST+ command line tool blastn instead of the legacy BLAST tool
> megablast... would that change be welcome?
Here is a fork of galaxy-central which updates megablast_wrapper.py
to actually use BLAST+, which seems to work for me:
Follow up change to update both the XML and py files to use the
new BLAST+ arguments for the filter (yes/no instead of T/F) and
update the list of columns in the documentation:
Note that both 'legacy' BLAST 2.2.22 and BLAST+ 2.2.24 both
output 12 columns in tabular mode, so I think the old XML wrapper
documentaion about 12 columns is wrong or was at least out of date.
These updates are on my branch 'megablast'.
Could someone review these changes for possible inclusion in
Galaxy? Would you prefer me to prepare a single patch file?