# HG changeset patch
# User peterjc
# Date 1375116949 14400
# Node ID 8615fd8abc04a57eb5a17785a61e4f299b8f53be
# Parent b3a3ba0c1d47345d1bdf49df80f3df5b0450f69c
Uploaded v0.0.16, moving to MIT license and development on GitHub.
No functional changes.
diff -r b3a3ba0c1d47 -r 8615fd8abc04 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Mon Jul 29 12:55:49 2013 -0400
@@ -0,0 +1,124 @@
+Galaxy datatypes for NCBI BLAST+ suite
+======================================
+
+These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
+Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
+Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
+
+See the licence text below.
+
+Note that these files (and the associated BLAST+ wrappers) were originally
+distributed as part of the main Galaxy repository, but as of August 2012 moved
+to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
+wrappers). My thanks to Dannon Baker from the Galaxy development team for his
+assistance with this.
+
+
+History
+=======
+
+These versions numbers initially matched those for 'ncbi_blast_plus', but are
+not used explicitly in the datatypes themselves.
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.11 - Final revision as part of the Galaxy main repository, and the
+ first release via the Tool Shed
+v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
+v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
+ (based on work by Edward Kirton)
+v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
+ BLAST database files (contribution from Nicola Soranzo)
+v0.0.16 - Adopt standard MIT License.
+ - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
+======= ======================================================================
+
+
+Installation
+============
+
+Doing this automatically via the Galaxy Tool Shed is probably simplest.
+
+
+Manual Installation
+===================
+
+Normally you would install this via the Galaxy ToolShed, which would move
+the provided blast.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::
+
+
+
+
+
+and later in the sniffer section::
+
+
+
+Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
+the blast.py file provided in this tar-ball. Finally add 'import blast' 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/galaxy_blast/issues or ask
+us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
+
+
+Developers
+==========
+
+BLAST+ datatypes and wrappers, and other tools were originally developed on the
+following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+As of July 2013, development is continuing on a dedicated GitHub repository:
+https://github.com/peterjc/galaxy_blast
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the following command from the blast_datatypes folder::
+
+ $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
+
+Check this worked::
+
+ $ tar -tzf blast_datatypes.tar.gz
+ README.rst
+ datatypes_conf.xml
+ blast.py
+
+For development, rather than having a local ToolShed running, I currently
+use a symlink from lib/galaxy/datatypes/blast.py to the actual file as
+described above.
+
+
+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 BLAST datatypes **only**. BLAST+
+and associated data files are available and licenced separately.
diff -r b3a3ba0c1d47 -r 8615fd8abc04 blast_datatypes.txt
--- a/blast_datatypes.txt Wed Mar 20 10:39:27 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,111 +0,0 @@
-Galaxy datatypes for NCBI BLAST+ suite
-======================================
-
-These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
-Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
-Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
-
-See the licence text below.
-
-Note that these files (and the associated BLAST+ wrappers) were originally
-distributed as part of the main Galaxy repository, but as of August 2012 moved
-to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
-wrappers). My thanks to Dannon Baker from the Galaxy development team for his
-assistance with this.
-
-
-History
-=======
-
-These versions numbers match those for 'ncbi_blast_plus', but are not used
-explicitly in the datatypes themselves.
-
-v0.0.11 - Final revision as part of the Galaxy main repository, and the
- first release via the Tool Shed
-v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
-v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
- (based on work by Edward Kirton)
-v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
- BLAST database files (contribution from Nicola Soranzo)
-
-
-Installation
-============
-
-Doing this automatically via the Galaxy Tool Shed is probably simplest.
-
-
-Manual Installation
-===================
-
-Normally you would install this via the Galaxy ToolShed, which would move
-the provided blast.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:
-
-
-
-
-
-and later in the sniffer section:
-
-
-
-Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking
-the blast.py file provided in this tar-ball. Finally add 'import blast' near
-the start of file lib/galaxy/datatypes/registry.py (after the other import
-lines).
-
-
-Developers
-==========
-
-BLAST+ datatypes and wrappers, and other tools are being developed on the
-following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy tools/ncbi_blast_plus folder:
-
-$ tar -czf blast_datatypes.tar.gz blast_datatypes.txt datatypes_conf.xml blast.py
-
-Check this worked:
-
-$ tar -tzf blast_datatypes.tar.gz
-blast_datatypes.txt
-datatypes_conf.xml
-blast.py
-
-Note that the placement of these three files under tools/ncbi_blast_plus is
-arbitrary - this just puts them next to the tool wrappers which use them.
-
-For development, rather than having a local ToolShed running, I currently
-use a symlink from lib/galaxy/datatypes/blast.py to the actual file
-tools/ncbi_blast_plus/blast.py as described above.
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
-NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+
-and associated data files are available and licenced separately.