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Testing updated NCBI BLAST+ wrappers for version 2.5.0

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Testing updated NCBI BLAST+ wrappers for version 2.5.0

Peter Cock
Hello all,

I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
the wrapper is now at v0.2.00:

https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/

The main changes is this now depends on BLAST+ 2.5.0, and that is
available via either BioConda or the Tool Shed:

https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/

In order for the dependency to work smoothly on both BioConda
and the Tool Shed system, we have changed the package name
from "blast+" to just "blast". Given the NCBI stopped updated the
original "legacy" BLAST some time ago, when combined with the
version number this is no longer ambiguous.

Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0
required updating lots of the test files for NCBI changes, including
dropping the GI numbers in many outputs, expanding the percentage
identity field from 2dp to 3dp, and also changing how -parse_deflines
works with tabular output.

The wrappers (deliberately) do not yet offer any new functionality
added in the recent NCBI BLAST+ updates, in particular BLAST
XML v2 is not yet available as an output with a datatype in Galaxy.

At this point I would welcome feedback from those of you using the
BLAST+ wrappers - including if you were able to install this with the
dependencies from BioConda or the traditional Tool Shed packages.

Once I'm confident that this is all OK, I will update the main Tool Shed
(and think about adding new functionality in 2017).

Thank you all,

Peter
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Re: Testing updated NCBI BLAST+ wrappers for version 2.5.0

Peter Cock
This just went live on the main tool shed:

https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/

You can report issues here or on GitHub at:

https://github.com/peterjc/galaxy_blast/issues

Thanks,

Peter

On Thu, Dec 8, 2016 at 11:35 AM, Peter Cock <[hidden email]> wrote:

> Hello all,
>
> I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
> the wrapper is now at v0.2.00:
>
> https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>
> The main changes is this now depends on BLAST+ 2.5.0, and that is
> available via either BioConda or the Tool Shed:
>
> https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
>
> In order for the dependency to work smoothly on both BioConda
> and the Tool Shed system, we have changed the package name
> from "blast+" to just "blast". Given the NCBI stopped updated the
> original "legacy" BLAST some time ago, when combined with the
> version number this is no longer ambiguous.
>
> Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0
> required updating lots of the test files for NCBI changes, including
> dropping the GI numbers in many outputs, expanding the percentage
> identity field from 2dp to 3dp, and also changing how -parse_deflines
> works with tabular output.
>
> The wrappers (deliberately) do not yet offer any new functionality
> added in the recent NCBI BLAST+ updates, in particular BLAST
> XML v2 is not yet available as an output with a datatype in Galaxy.
>
> At this point I would welcome feedback from those of you using the
> BLAST+ wrappers - including if you were able to install this with the
> dependencies from BioConda or the traditional Tool Shed packages.
>
> Once I'm confident that this is all OK, I will update the main Tool Shed
> (and think about adding new functionality in 2017).
>
> Thank you all,
>
> Peter
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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