comparison tools/ncbi_blast_plus/README.rst @ 11:4c4a0da938ff draft

Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.

10:70e7dcbf6573

These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 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
with this.

These wrappers are available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

Automated Installation
======================

Galaxy should be able to automatically install the dependencies, i.e. the
'blast_datatypes' repository which defines the BLAST XML file format
('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and
'blastdbn').

You must tell Galaxy about any system level BLAST databases using configuration
files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein
databases like NR), and blastdb_d.loc (protein domain databases like CDD or
SMART) which are located in the tool-data/ folder. Sample files are included

Manual Installation
===================

For those not using Galaxy's automated installation from the Tool Shed, put
the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML
files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample
in order to run the unit tests). For example, use::

  <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />
    <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
  </section>

You will also need to install 'blast_datatypes' from the Tool Shed. This
defines the BLAST XML file format ('blastxml') and protein and nucleotide
BLAST databases composite file formats ('blastdbp' and 'blastdbn').

As described above for an automated installation, you must also tell Galaxy
about any system level BLAST databases using the tool-data/blastdb*.loc files.

You must install the NCBI BLAST+ standalone tools somewhere on the system
path. Currently the unit tests are written using "BLAST 2.2.26+".

Run the functional tests (adjusting the section identifier to match your
tool_conf.xml.sample file)::

    ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools


History

        - Tweak dependency on blast_datatypes to also work on Test Tool Shed.
        - Dependency on new package_blast_plus_2_2_26 in Tool Shed.
        - Adopted standard MIT License.
        - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
        - Updated citation information (Cock et al. 2013).
======= ======================================================================


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

https://github.com/peterjc/galaxy_blast

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
the following command from the GitHub repository root folder::

    $ ./ncbi_blast_plus/make_ncbi_blast_plus.sh

This simplifies ensuring a consistent set of files is bundled each time,
including all the relevant test files.


Licence (MIT)
=============

11:4c4a0da938ff

These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 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
with this.

These wrappers are available from the Galaxy Tool Shed at:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus

Automated Installation
======================

Galaxy should be able to automatically install the dependencies, i.e. the
``blast_datatypes`` repository which defines the BLAST XML file format
(``blastxml``) and protein and nucleotide BLAST databases (``blastdbp`` and
``blastdbn``).

You must tell Galaxy about any system level BLAST databases using configuration
files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein
databases like NR), and blastdb_d.loc (protein domain databases like CDD or
SMART) which are located in the tool-data/ folder. Sample files are included

Manual Installation
===================

For those not using Galaxy's automated installation from the Tool Shed, put
the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the
XML files to your ``tool_conf.xml`` as normal (and do the same in
``tool_conf.xml.sample`` in order to run the unit tests). For example, use::

  <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />
    <tool file="ncbi_blast_plus/ncbi_dustmasker_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />
    <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
  </section>

You will also need to install ``blast_datatypes`` from the Tool Shed. This
defines the BLAST XML file format (``blastxml``) and protein and nucleotide
BLAST databases composite file formats (``blastdbp`` and ``blastdbn``):

* http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes

As described above for an automated installation, you must also tell Galaxy
about any system level BLAST databases using the ``tool-data/blastdb*.loc``
files.

You must install the NCBI BLAST+ standalone tools somewhere on the system
path. Currently the unit tests are written using "BLAST 2.2.28+".

Run the functional tests (adjusting the section identifier to match your
``tool_conf.xml.sample`` file)::

    ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools


History

        - Tweak dependency on blast_datatypes to also work on Test Tool Shed.
        - Dependency on new package_blast_plus_2_2_26 in Tool Shed.
        - Adopted standard MIT License.
        - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
        - Updated citation information (Cock et al. 2013).
v0.0.21 - Use macros to simplify the XML wrappers.
        - Added wrapper for dustmasker
        - Enabled masking for makeblastdb
        - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes
          defined in updated blast_datatypes on Galaxy ToolShed.
        - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26
        - Now depends on package_blast_plus_2_2_27 in ToolShed
v0.0.22 - More use macros to simplify the wrappers
        - Set number of threads via $GALAXY_SLOTS environment variable
        - More descriptive default output names
        - Tests require updated BLAST DB definitions (blast_datatypes v0.0.18)
        - Pre-check for duplicate identifiers in makeblastdb wrapper.
        - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27
        - Now depends on package_blast_plus_2_2_28 in ToolShed
        - Extended tabular output includes 'salltitles' as column 25.
======= ======================================================================


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

https://github.com/peterjc/galaxy_blast

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
the following command from the GitHub repository root folder::

    $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh

This simplifies ensuring a consistent set of files is bundled each time,
including all the relevant test files.

When updating the version of BLAST+, many of the sample data files used for
the unit tests must be regenerated. This script automates that task::

    $ tools/ncbi_blast_plus/update_test_files.sh


Licence (MIT)
=============