comparison tools/seq_rename/README.rst @ 3:e1398f2ba9fe draft default tip

v0.0.8 galaxy_sequence_utils dependency etc

2:7c0642fc57ad

Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
=========================================================

This tool is copyright 2011-2013 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 (using Biopython library functions) to rename
sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as

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

There are just two files to install to use this tool from within Galaxy:

* seq_rename.py (the Python script)
* seq_rename.xml (the Galaxy tool definition)

The suggested location is in a dedicated tools/seq_rename folder.

You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
tool. One suggested location is in the filters section. Simply add the line::

    <tool file="seq_rename/seq_rename.xml" />

If you wish to run the unit tests, also add this to tools_conf.xml.sample
and move/copy the test-data files under Galaxy's test-data folder. Then::

    $ ./run_functional_tests.sh -id seq_rename

You will also need to install Biopython 1.54 or later. That's it.


History

        - Use reStructuredText for this README file.
        - Adopt standard MIT License.
        - Updated citation information (Cock et al. 2013).
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
        - Renamed folder and adopted README.rst naming.
======= ======================================================================


Developers
==========

http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools

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

    $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta

Check this worked::

    $ tar -tzf seq_rename.tar.gz
    tools/seq_rename/README.rst
    tools/seq_rename/seq_rename.py
    tools/seq_rename/seq_rename.xml
    tools/seq_rename/repository_dependencies.xml
    test-data/four_human_proteins.fasta
    test-data/four_human_proteins.rename.tabular
    test-data/four_human_proteins.rename.fasta


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

3:e1398f2ba9fe

Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
=========================================================

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 (using Biopython library functions) to rename
sequences from a FASTA, QUAL, FASTQ, or SFF file based on an ID mapping gives as

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

There are just two files to install to use this tool from within Galaxy:

* ``seq_rename.py`` (the Python script)
* ``seq_rename.xml`` (the Galaxy tool definition)

The suggested location is in a dedicated ``tools/seq_rename`` folder.

You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
tool. One suggested location is in the filters section. Simply add the line::

    <tool file="seq_rename/seq_rename.xml" />

If you wish to run the unit tests, also move/copy the ``test-data/`` files
under Galaxy's ``test-data/`` folder. Then::

    $ ./run_tests.sh -id seq_rename

You will also need to install Biopython 1.54 or later. That's it.


History

        - Use reStructuredText for this README file.
        - Adopt standard MIT License.
        - Updated citation information (Cock et al. 2013).
        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
        - Renamed folder and adopted README.rst naming.
v0.0.5  - Correct automated dependency definition.
v0.0.6  - Simplified XML to apply input format to output data.
        - Tool definition now embeds citation information.
        - If white space is found in the requested tabular field then only
          the first word is used as the identifier (with a warning to stderr).
v0.0.7  - Use the ``format_source=...`` tag.
        - Reorder XML elements (internal change only).
        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
        - Capture the tool version via Galaxy (bug fix).
v0.0.8  - Updated to point at Biopython 1.67 (latest version in Tool Shed).
        - Explicit dependency on ``galaxy_sequence_utils``.
        - Python style updates (internal change only).
======= ======================================================================


Developers
==========

http://bitbucket.org/peterjc/galaxy-central/src/tools

Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools

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/pico_galaxy/tools/seq_rename/
    ...

or::

    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_rename/
    ...

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

    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_rename/
    ...
    $ tar -tzf shed_upload.tar.gz 
    test-data/four_human_proteins.fasta
    test-data/four_human_proteins.rename.fasta
    test-data/four_human_proteins.rename.tabular
    tools/seq_rename/README.rst
    tools/seq_rename/seq_rename.py
    tools/seq_rename/seq_rename.xml
    tools/seq_rename/tool_dependencies.xml


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