changeset 4:bedf9f58c025 draft

Uploaded
author jasper
date Fri, 03 Feb 2017 12:51:03 -0500
parents f2e2a5cf8911
children 5cc3960f7c3c
files README.rst
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+Galaxy tool to back-translate a protein alignment to nucleotides
+================================================================
+
+This tool is copyright 2012-2015 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
+load a protein alignment, and matching nucleotide FASTA file of unaligned
+sequences, which are threaded onto the protein alignment in order to produce
+a codon aware nucleotide alignment - which can be viewed as a back translation.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans
+
+The underlying Python script can also be used outside of Galaxy, for
+details run::
+
+    $ python align_back_trans.py
+
+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:
+
+* ``align_back_trans.py`` (the Python script)
+* ``align_back_trans.xml`` (the Galaxy tool definition)
+
+The suggested location is in a dedicated ``tools/align_back_trans`` 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 multiple alignments section. Simply
+add the line::
+
+    <tool file="align_back_trans/align_back_trans.xml" />
+
+You will also need to install Biopython 1.62 or later.
+
+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 align_back_trans
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version, based on a previously written Python script
+v0.0.2  - Optionally check the translation is consistent
+v0.0.3  - First official release
+v0.0.4  - Simplified XML to apply input format to output data.
+        - Fixed error message when sequence length not a multiple of three.
+v0.0.5  - More explicit error messages when seqences lengths do not match.
+        - Tool definition now embeds citation information.
+v0.0.6  - Reorder XML elements (internal change only).
+        - Use ``format_source=...`` tag.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+======= ======================================================================
+
+
+Developers
+==========
+
+This script was initially developed on this repository:
+https://github.com/peterjc/picobio/blob/master/align/align_back_trans.py
+
+With the addition of a Galaxy wrapper, developement moved here:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
+
+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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+
+or::
+
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/demo_nucs.fasta
+    test-data/demo_nucs_trailing_stop.fasta
+    test-data/demo_prot_align.fasta
+    test-data/demo_nuc_align.fasta
+    tools/align_back_trans/README.rst
+    tools/align_back_trans/align_back_trans.py
+    tools/align_back_trans/align_back_trans.xml
+    tools/align_back_trans/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.