comparison tools/ncbi_blast_plus/README.rst @ 20:3034ce97dd33 draft

Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.

19:7f3c448e119b

Galaxy wrappers for NCBI BLAST+ suite
=====================================

These wrappers are copyright 2010-2014 by Peter Cock (The James Hutton Institute,
UK) and additional contributors including Edward Kirton, John Chilton,
Nicola Soranzo, Jim Johnson, and Bjoern Gruening.

See the licence text below.

Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+),
and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``).

Note that these wrappers (and the associated datatypes) were originally
distributed as part of the main Galaxy repository, but as of August 2012
moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``).
My thanks to Dannon Baker from the Galaxy development team for his assistance

``$GALAXY_SLOTS`` environment variable. This should be set automatically by
Galaxy via your job runner settings, which allows you to (for example) allocate
four cores to each BLAST job.

In addition, the BLAST+ wrappers also support high level parallelism by task
splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini``
configuration file. Essentially, the FASTA input query files are broken up into
batches of 1000 sequences, a separate BLAST child job is run for each chunk,
and then the BLAST output files are merged (in order). This is transparent
for the end user.

History

        - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30.
v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported
          on the Tool Shed test framework, but that is not currently in use).
        - Fixed macro problem with version field in blastxml_to_tabular.xml
          (contribution from Bjoern Gruening and Daniel Blankenberg).
======= ======================================================================


Bug Reports
===========

20:3034ce97dd33

Galaxy wrappers for NCBI BLAST+ suite
=====================================

These wrappers are copyright 2010-2016 by Peter Cock (The James Hutton Institute,
UK) and additional contributors including Edward Kirton, John Chilton,
Nicola Soranzo, Jim Johnson, and Bjoern Gruening.

See the licence text below.

Currently tested with NCBI BLAST+ 2.2.31, and does not work with the NCBI
'legacy' BLAST suite (e.g. ``blastall``).

Note that these wrappers (and the associated datatypes) were originally
distributed as part of the main Galaxy repository, but as of August 2012
moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``).
My thanks to Dannon Baker from the Galaxy development team for his assistance

``$GALAXY_SLOTS`` environment variable. This should be set automatically by
Galaxy via your job runner settings, which allows you to (for example) allocate
four cores to each BLAST job.

In addition, the BLAST+ wrappers also support high level parallelism by task
splitting if ``use_tasked_jobs = True`` is enabled in the ``config/galaxy.ini``
configuration file (previously ``universe_wsgi.ini`` on older versions of
Galaxy). Essentially, the FASTA input query files are broken up into
batches of 1000 sequences, a separate BLAST child job is run for each chunk,
and then the BLAST output files are merged (in order). This is transparent
for the end user.

History

        - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30.
v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported
          on the Tool Shed test framework, but that is not currently in use).
        - Fixed macro problem with version field in blastxml_to_tabular.xml
          (contribution from Bjoern Gruening and Daniel Blankenberg).
v0.1.08 - Allow searching against multiple locally installed databases
          (contribution from Gildas Le Corguillé and Emma Prudent).
        - Minor XML and Python style changes (internal change only).
        - Set ``allow_duplicate_entries="False"`` in sample configuration file
	  ``tool_data_table_conf.xml``.
        - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan).
======= ======================================================================


Bug Reports
===========