diff tools/sample_seqs/README.rst @ 0:3a807e5ea6c8 draft

Uploaded v0.0.1

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+Galaxy tool to find ORFs or simple CDSs
+=======================================
+
+This tool is copyright 2014 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 sub-sample sequence files (in a range of formats including FASTA, FASTQ,
+and SFF). This can be useful for preparing a small sample of data to test
+or time a new pipeline, or for reducing the read coverage in a de novo
+assembly.
+
+This tool is available from the Galaxy Tool Shed at:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
+
+
+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:
+
+* ``sample_seqs.py`` (the Python script)
+* ``sample_seqs.xml`` (the Galaxy tool definition)
+
+The suggested location is in a dedicated ``tools/sample_seqs`` 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="sample_seqs/sample_seqs.xml" />
+
+You will also need to install Biopython 1.62 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 sample_seqs
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools are being developed on this GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
+
+Check this worked::
+
+    $ tar -tzf sample_seqs.tar.gz
+    tools/sample_seqs/README.rst
+    tools/sample_seqs/sample_seqs.py
+    tools/sample_seqs/sample_seqs.xml
+    tools/sample_seqs/tool_dependencies.xml
+    test-data/ecoli.fastq
+    test-data/ecoli.sample_N100.fastq
+    test-data/get_orf_input.Suis_ORF.prot.fasta
+    test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.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.