diff tools/seq_primer_clip/README.rst @ 2:ee5acea162a7 draft

Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency

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+Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
+===========================================================
+
+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 the Galaxy library functions and
+Biopython). It is available from the Galaxy Tool Shed here:
+http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
+
+
+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:
+
+* seq_primer_clip.py (the Python script)
+* seq_primer_clip.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/seq_primer_clip folder. You will also
+need to modify the tools_conf.xml file to tell Galaxy to offer the tool::
+
+  <tool file="seq_primer_clip/seq_primer_clip.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_primer_clip
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (not publicly released)
+v0.0.2  - Sort primers by length (longest and therefore most specific first)
+v0.0.3  - Consider missing bases at start/end of read as mismatches
+v0.0.4  - Apply minimum length to sequences with no match too
+v0.0.5  - Count clipped & non-matched short reads separately, length bug fixes
+v0.0.6  - Added some functional tests
+v0.0.7  - Added error check for bad filename arguments
+v0.0.8  - Record version of Python script when run from Galaxy.
+        - Check for errors using Python script's return code.
+v0.0.9  - Moved test data to workaround Galaxy Tool Shed limititation.
+v0.0.10 - Include links to Tool Shed in help text and this README file.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Automated installation of Biopython dependency.
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+        - Renamed folder and adopted README.rst naming.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branches:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy
+
+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_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/repository_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30*
+
+Check this worked::
+
+    $ tar -tzf seq_primer_clip.tar.gz
+    tools/seq_primer_clip/README.rst
+    tools/seq_primer_clip/seq_primer_clip.xml
+    tools/seq_primer_clip/seq_primer_clip.py
+    tools/seq_primer_clip/repository_dependencies.xml
+    test-data/dop_primers.fasta
+    test-data/MID4_GLZRM4E04_rnd30.fasta
+    test-data/MID4_GLZRM4E04_rnd30.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_fclip.fasta
+    test-data/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_fclip.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.fasta
+    test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
+    test-data/MID4_GLZRM4E04_rnd30.sff
+
+
+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.