diff tools/samtools_depad/README.rst @ 0:2d303f2e09e0 draft

Uploaded v0.0.1, previously only on the Test Tool Shed

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+++ b/tools/samtools_depad/README.rst	Fri Nov 21 06:37:20 2014 -0500
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+Galaxy wrapper for samtools depad
+=================================
+
+This wrapper 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.
+
+This is a wrapper for part of the command line samtools suite, v0.1.19
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+samtools 0.1.19 if required.
+
+
+Manual Installation
+===================
+
+This expects samtools to be on the $PATH, and was tested using v0.1.19.
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a ``tools/samtools_depad`` folder:
+
+* ``samtools_depad.xml`` (the Galaxy tool definition)
+* ``samtools_depad.py`` (the Python wrapper script)
+* ``README.rst`` (this file)
+
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
+the tool. Just add the line, perhaps under the NGS tools section::
+
+  <tool file="samtools_depad/samtools_depad.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 samtools_depad
+
+That's it.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+======= ======================================================================
+
+
+Developers
+==========
+
+Development is on this GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf samtools_depad.tar.gz tools/samtools_depad/README.rst tools/samtools_depad/samtools_depad.xml tools/samtools_depad/samtools_depad.py tools/samtools_depad/tool_dependencies.xml test-data/sam_spec_padded.fasta test-data/sam_spec_padded.sam test-data/sam_spec_padded.bam test-data/sam_spec_padded.depad.bam
+
+Check this worked::
+
+    $ tar -tzf samtools_depad.tar.gz
+    tools/samtools_depad/README.rst
+    tools/samtools_depad/samtools_depad.xml
+    tools/samtools_depad/samtools_depad.py
+    tools/samtools_depad/tool_dependencies.xml
+    test-data/sam_spec_padded.fasta
+    test-data/sam_spec_padded.sam
+    test-data/sam_spec_padded.bam
+    test-data/sam_spec_padded.depad.bam
+
+
+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.
+
+NOTE: This is the licence for the Galaxy Wrapper only.
+samtools is available and licenced separately.