Mercurial > repos > peterjc > mira_datatypes

--- a/README.rst	Fri Aug 11 13:35:02 2017 -0400
+++ b/README.rst	Mon Aug 14 12:33:11 2017 -0400
@@ -1,11 +1,112 @@
-Galaxy packages for MIRA
-========================
+Galaxy datatypes for MIRA Assembly Format (MAF)
+===============================================
+
+These Galaxy datatypes are copyright 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 code defines a 'mira' datatype within Galaxy for the MIRA Assembly Format
+(specifically v2 of the format introduced by MIRA 4.0 and the development
+preview releases of MIRA v3.9). See http://chevreux.org/projects_mira.html
+and https://sourceforge.net/projects/mira-assembler/ for background.
+
+This format is not to be confused with the existing 'maf' datatype within Galaxy
+for the unrelated Multiple (sequence) Alignment Format (MAF).
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes
+
+
+History
+=======

-The code for my Galaxy wrappers for MIRA and associated packages has been
-moved to a new repository:
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - First public release
+======= ======================================================================
+
+
+Installation
+============
+
+Doing this automatically via the Galaxy Tool Shed is probably simplest, and will
+happen automatically as a dependency of the Galaxy wrapper for MIRA v4.0.
+
+
+Manual Installation
+===================
+
+Normally you would install this via the Galaxy ToolShed, which would move
+the provided mira.py file into a suitable location and process the
+``datatypes_conf.xml`` entry to be combined with your local configuration.
+
+However, if you really want to this should work for a manual install. Add
+the following lines to the ``datatypes_conf.xml`` file in the Galaxy main folder::
+
+    <datatype extension="mira" type="galaxy.datatypes.mira:MiraAssemblyFormat" mimetype="text/plain" display_in_upload="true"/>
+
+and later in the sniffer section::
+
+    <sniffer type="galaxy.datatypes.mira:MiraAssemblyFormat"/>

-https://github.com/peterjc/galaxy_mira/
+Also create the file ``lib/galaxy/datatypes/mira.py`` by moving, copying or linking
+the mira.py file provided in this tar-ball.  Finally add ``import mira`` near
+the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import
+lines).
+
+
+Bug Reports
+===========
+
+You can file an issue here https://github.com/peterjc/pico_galaxy/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+
+
+Developers
+==========
+
+Development is done on this GitHub repository:
+https://github.com/peterjc/pico_galaxy
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the following command from the ``mira_datatypes`` folder::
+
+    $ tar -czf mira_datatypes.tar.gz README.rst datatypes_conf.xml mira.py
+
+Check this worked::

-The tools, datatypes and packages remain available from the Galaxy Tool Shed:
+    $ tar -tzf mira_datatypes.tar.gz
+    README.rst
+    datatypes_conf.xml
+    mira.py
+
+For development, rather than having a local ToolShed running, I currently
+use a symlink from ``lib/galaxy/datatypes/mira.py`` to the actual file as
+described above.
+
+
+Licence (MIT)
+=============

-http://toolshed.g2.bx.psu.edu/view/peterjc/
+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 MIRA datatypes **only**. MIRA itself
+is available and licenced separately.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Mon Aug 14 12:33:11 2017 -0400
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<datatypes>
+    <datatype_files>
+        <datatype_file name="mira.py"/>
+    </datatype_files>
+    <registration>
+        <datatype extension="mira" type="galaxy.datatypes.mira:MiraAssemblyFormat" mimetype="text/plain" display_in_upload="true"/>
+    </registration>
+    <sniffers>
+        <sniffer type="galaxy.datatypes.mira:MiraAssemblyFormat"/>
+    </sniffers>
+</datatypes>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mira.py	Mon Aug 14 12:33:11 2017 -0400
@@ -0,0 +1,48 @@
+"""
+MiraAssemblyFormat class for the 'mira' format within Galaxy
+"""
+
+from galaxy.datatypes.data import Text
+
+
+class MiraAssemblyFormat(Text):
+    """MIRA Assembly Format  data"""
+    file_ext = "mira"
+
+    def sniff(self, filename):
+        """Determines whether the file is a MIRA Assembly Format file.
+
+        Note currently this only detects MIRA Assembly Format v2.0,
+        as used in MIRA v3.9 and v4.0.
+
+        It does not detect MIRA Assembly Format v1 as used in both
+        MIRA v3.2 and v3.4.
+        """
+        h = open(filename)
+        line = h.readline()
+        if line.rstrip() != "@Version\t2\t0":
+            h.close()
+            return False
+        line = h.readline()
+        if line.rstrip() != "@Program\tMIRALIB":
+            h.close()
+            return False
+        return True
+
+    def merge(split_files, output_file):
+        """Merging multiple MIRA files is non-trivial and may not be possible..."""
+        if len(split_files) == 1:
+            # For one file only, use base class method (move/copy)
+            return Text.merge(split_files, output_file)
+        if not split_files:
+            raise ValueError("Given no MIRA, %r, to merge into %s"
+                             % (split_files, output_file))
+        raise NotImplementedError("Merging MIRA Assembly Files has not been implemented")
+    merge = staticmethod(merge)
+
+    def split(cls, input_datasets, subdir_generator_function, split_params):
+        """Split a MIRA Assembly File (not implemented for now)."""
+        if split_params is None:
+            return None
+        raise NotImplementedError("Can't yet split a MIRA Assembly Format file")
+    merge = staticmethod(merge)