Mercurial > repos > peterjc > mira_datatypes

--- a/README.rst	Mon Nov 19 12:15:01 2018 -0500
+++ b/README.rst	Mon Nov 19 12:44:09 2018 -0500
@@ -1,112 +1,11 @@
-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
-=======
+Galaxy packages for MIRA
+========================

-======= ======================================================================
-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"/>
+The code for my Galaxy wrappers for MIRA and associated packages has been
+moved to a new repository:

-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::
+https://github.com/peterjc/galaxy_mira/

-    $ 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)
-=============
+The tools, datatypes and packages remain available from the Galaxy Tool Shed:

-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.
+http://toolshed.g2.bx.psu.edu/view/peterjc/
--- a/datatypes_conf.xml	Mon Nov 19 12:15:01 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?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>
--- a/mira.py	Mon Nov 19 12:15:01 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-"""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):
-        """Determine if 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):
-        """Merge MIRA assembly files (not implemented).
-
-        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)