comparison tools/blast_rbh/README.rst @ 4:d8d9a9069586 draft

v0.1.11 using BLAST+ 2.5.0 and Biopython 1.67

3:9ba8ebb636f4

Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper
==========================================================

This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

This tool is a short Python script to run reciprocal BLAST searches on a
pair of sequence files, and extract the reciprocal best hits. The script

v0.1.6  - Offer the new blastp-fast task added in BLAST+ 2.2.30.
        - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
v0.1.7  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Updated citation information with GigaScience paper.
v0.1.8  - Updated to depend on  NCBI BLAST+ 2.2.31 via ToolShed install.
======= ======================================================================


Developers
==========

For pushing a release to the test or main "Galaxy Tool Shed", use the following
Planemo commands (which requires you have set your Tool Shed access details in
``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast_rbh/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/four_human_proteins.fasta
    test-data/k12_edited_proteins.fasta
    test-data/k12_ten_proteins.fasta

4:d8d9a9069586

Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper
==========================================================

This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
See the licence text below.

This tool is a short Python script to run reciprocal BLAST searches on a
pair of sequence files, and extract the reciprocal best hits. The script

v0.1.6  - Offer the new blastp-fast task added in BLAST+ 2.2.30.
        - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
v0.1.7  - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Updated citation information with GigaScience paper.
v0.1.8  - Updated to depend on NCBI BLAST+ 2.2.31 via ToolShed install.
v0.1.9  - Updates to the command line API for the Python script.
        - PEP8 style updates to the Python script (internal change only).
        - Fix parameter help text which was not being displayed.
v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
        - Update Biopython dependency.
        - Tweak Python script to work under Python 2 or Python 3.
======= ======================================================================


Developers
==========

For pushing a release to the test or main "Galaxy Tool Shed", use the following
Planemo commands (which requires you have set your Tool Shed access details in
``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

    $ planemo shed_update -t testtoolshed --check_diff tools/blast_rbh/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff tools/blast_rbh/
    ...

To just build and check the tar ball, use::

    $ planemo shed_upload --tar_only tools/blast_rbh/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/four_human_proteins.fasta
    test-data/k12_edited_proteins.fasta
    test-data/k12_ten_proteins.fasta