This should be straightforward using the Galaxy Tool Shed, which should be
able to automatically install the dependency on Biopython, and then install
this tool and run its unit tests.
There are just two files to install to use this tool from within Galaxy:
- seq_filter_by_id.py (the Python script)
- seq_filter_by_id.xml (the Galaxy tool definition)
The suggested location is a dedicated tools/seq_filter_by_id 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_filter_by_id/seq_filter_by_id.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_filter_by_id
You will also need to install Biopython 1.54 or later. That's it.
- Initial version, combining three separate scripts for each file format.
- Record script version when run from Galaxy.
- Faster FASTA code which preserves the original line wrapping.
- Basic unit test included.
- Check for errors using Python script's return code.
- Cope with malformed FASTA entries without an identifier.
- Link to Tool Shed added to help text and this documentation.
- Automated installation of the Biopython dependency.
- 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.
This script and related tools were initially developed on the following hg branches:
Development has now moved to a dedicated GitHub repository:
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_filter_by_id.tar.gz tools/seq_filter_by_id/README.rst tools/seq_filter_by_id/seq_filter_by_id.* tools/seq_filter_by_id/repository_dependencies.xml test-data/k12_ten_proteins.fasta test-data/k12_hypothetical.fasta test-data/k12_hypothetical.tabular
Check this worked:
$ tar -tzf seq_filter_by_id.tar.gz
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN