Automated Installation
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.
Manual Installation
There are just two files to install to use this tool from within Galaxy:
- get_orfs_or_cdss.py (the Python script)
- get_orfs_or_cdss.xml (the Galaxy tool definition)
The suggested location is in a dedicated tools/get_orfs_or_cdss 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="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
You will also need to install Biopython 1.65 or later (slightly older versions
should be fine, but will not have the latest NCBI genetic code tables).
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 get_orfs_or_cdss
That's it.
History
| Version |
Changes |
| v0.0.1 |
|
| v0.0.2 |
- Correct labelling issue on reverse strand.
- Use the new <stdio> settings in the XML wrappers to catch errors
|
| v0.0.3 |
- Include unit tests.
- Record Python script version when run from Galaxy.
|
| v0.0.4 |
- Link to Tool Shed added to help text and this documentation.
|
| v0.0.5 |
- Automated intallation of the Biopython dependency.
- Use reStructuredText for this README file.
- Adopt standard MIT License.
- Updated citation information (Cock et al. 2013).
- Renamed folder and adopted README.rst naming.
|
| v0.0.6 |
- Corrected automated dependency defintion.
|
| v0.0.7 |
- Tool definition now embeds citation information.
|
| v0.1.0 |
- Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
- Using optparse for the Python command line API (Eric Rasche).
- Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
|
| v0.1.1 |
- Reorder XML elements (internal change only).
|
| v0.2.0 |
- Tool now also outputs GFF3 formatted calls (Eric Rasche).
|
| v0.2.1 |
- Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
- Added NCBI genetic code table 24, Candidate Division SR1 and
Gracilibacteria.
|
| v0.2.2 |
- Use <command detect_errors="aggressive"> (internal change only).
- Single quote command line arguments (internal change only).
|
| v0.2.3 |
- Python 3 compatible print function.
|
Developers
This script and related tools were initially developed on the following hg branch:
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 tools/get_orfs_or_cdss/
...
or:
$ planemo shed_update -t toolshed --check_diff tools/get_orfs_or_cdss/
...
To just build and check the tar ball, use:
$ planemo shed_upload --tar_only tools/get_orfs_or_cdss/
...
$ tar -tzf shed_upload.tar.gz
test-data/Ssuis.fasta
test-data/get_orf_input.Suis_ORF.bed
test-data/get_orf_input.Suis_ORF.nuc.fasta
test-data/get_orf_input.Suis_ORF.prot.fasta
test-data/get_orf_input.fasta
test-data/get_orf_input.t11_bed_out.bed
test-data/get_orf_input.t11_nuc_out.fasta
test-data/get_orf_input.t11_open_bed_out.bed
test-data/get_orf_input.t11_open_nuc_out.fasta
test-data/get_orf_input.t11_open_prot_out.fasta
test-data/get_orf_input.t11_prot_out.fasta
test-data/get_orf_input.t1_bed_out.bed
test-data/get_orf_input.t1_nuc_out.fasta
test-data/get_orf_input.t1_prot_out.fasta
tools/get_orfs_or_cdss/get_orfs_or_cdss.py
tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
tools/get_orfs_or_cdss/README.rst
tools/get_orfs_or_cdss/tool_dependencies.xml
Licence (MIT)
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
THE SOFTWARE.
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