diff tools/get_orfs_or_cdss/README.rst @ 5:5208c15805ec draft

Uploaded v0.0.5 dependant on Biopython 1.62

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+Galaxy tool to find ORFs or simple CDSs
+=======================================
+
+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 (MIT licence).
+
+This tool is a short Python script (using Biopython library functions)
+to search nucleotide sequences for open reading frames (ORFs) or coding
+sequences (CDSs) where the first potential start codon is used. See the
+help text in the XML file for more information.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
+
+See also the EMBOSS tool ``getorf`` which offers similar functionality and
+has also been wrapped for use within Galaxy.
+
+
+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 1.54 or later. If you want to run
+the unit tests, include this line in tools_conf.xml.sample and the sample
+FASTA files under the test-data directory. Then::
+
+    ./run_functional_tests.sh -id get_orfs_or_cdss
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+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.
+======= ======================================================================
+
+
+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 making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/repository_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta
+
+Check this worked::
+
+    $ tar -tzf get_orfs_or_cdss.tar.gz
+    tools/get_orfs_or_cdss/README.rst
+    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/repository_dependencies.xml
+    test-data/get_orf_input.fasta
+    test-data/get_orf_input.Suis_ORF.nuc.fasta
+    test-data/get_orf_input.Suis_ORF.prot.fasta
+    test-data/get_orf_input.t11_nuc_out.fasta
+    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_nuc_out.fasta
+    test-data/get_orf_input.t1_prot_out.fasta
+    test-data/Ssuis.fasta
+
+
+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.