blast_datatypes: README.rst annotate

annotate README.rst @ 19:db2480de852e draft default tip

"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty"

author	peterjc
date	Fri, 21 Aug 2020 12:39:02 +0000
parents	63befb860c3e
children

rev	line source
19 db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	1 Galaxy datatypes for NCBI BLAST+ suite (OBSOLETE)
db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	2 =================================================
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	3
11 236046d1d441 Uploaded v0.0.19a, README tweaks peterjc parents: 10 diff changeset	4 These Galaxy datatypes are copyright 2010-2014 by Peter Cock (The James Hutton
236046d1d441 Uploaded v0.0.19a, README tweaks peterjc parents: 10 diff changeset	5 Institute, UK) and additional contributors including Edward Kirton, Nicola
236046d1d441 Uploaded v0.0.19a, README tweaks peterjc parents: 10 diff changeset	6 Soranzo, and Bjoern Gruening.
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	7
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	8 See the licence text below.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	9
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	10 Note that these files (and the associated BLAST+ wrappers) were originally
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	11 distributed as part of the main Galaxy repository, but as of August 2012 moved
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	12 to the Galaxy Tool Shed as 'blast_datatypes' (and 'ncbi_blast_plus' for the
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	13 wrappers). My thanks to Dannon Baker from the Galaxy development team for his
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	14 assistance with this.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	15
19 db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	16 The datatypes returned to the main Galaxy repository and were including in the
db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	17 October 2016 release. There have been minor changes there since. These copies
db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	18 are now obsolete.
db2480de852e "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit f726ee4fbfef077d2ffe7e1a67eee254babb7841-dirty" peterjc parents: 16 diff changeset	19
8 7ceb2ae30ff4 Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes peterjc parents: 7 diff changeset	20 It is available from the Galaxy Tool Shed at:
7ceb2ae30ff4 Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes peterjc parents: 7 diff changeset	21 http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
7ceb2ae30ff4 Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes peterjc parents: 7 diff changeset	22
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	23
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	24 History
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	25 =======
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	26
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	27 These versions numbers initially matched those for 'ncbi_blast_plus', but are
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	28 not used explicitly in the datatypes themselves.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	29
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	30 ======= ======================================================================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	31 Version Changes
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	32 ------- ----------------------------------------------------------------------
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	33 v0.0.11 - Final revision as part of the Galaxy main repository, and the
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	34 first release via the Tool Shed
11 236046d1d441 Uploaded v0.0.19a, README tweaks peterjc parents: 10 diff changeset	35 v0.0.13 - Uses ``blast.py`` instead of ``xml.py`` to define the datatypes
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	36 v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	37 (``blastdbp`` and ``blastdbn``, based on work by Edward Kirton)
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	38 v0.0.15 - Fixes a MetadataElement bug and includes more of the optional
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	39 BLAST database files (contribution from Nicola Soranzo)
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	40 v0.0.16 - Adopt standard MIT License.
8 7ceb2ae30ff4 Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes peterjc parents: 7 diff changeset	41 - Use reStructuredText for this README file.
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	42 - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
7 a44a7a5456e1 Uploaded v0.0.16a, Nucleotide database definition aware of MegaBLAST index superheader peterjc parents: 6 diff changeset	43 - Nucleotide database definition aware of MegaBLAST index superheader
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	44 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes
11 236046d1d441 Uploaded v0.0.19a, README tweaks peterjc parents: 10 diff changeset	45 (contribution from Nicola Soranzo)
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 8 diff changeset	46 v0.0.18 - Add retries to BLAST XML merge code.
e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 8 diff changeset	47 - Modify display_data method to allow unit tests to function.
12 da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	48 v0.0.19 - Add ``blastdbd`` datatype for BLAST protein domain databases, for use
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	49 with makeprofiledb and rpsblast (contribution from Bjoern Gruening).
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	50 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	51 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named
12 da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	52 as ``*.smp``), used as input files for makeprofiledb.
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	53 v0.0.20 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
13 e96b515847dd v0.0.21 - Updated citation information with GigaScience paper peterjc parents: 12 diff changeset	54 v0.0.21 - Updated citation information with GigaScience paper.
14 623a3fbe5340 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 3f6b5c953d522a724bbcd403bcb86f1e2757a556-dirty peterjc parents: 13 diff changeset	55 v0.0.22 - Removed unused imports in ``blast.py`` (internal change only).
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	56 ======= ======================================================================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	57
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	58
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	59 Installation
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	60 ============
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	61
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	62 Doing this automatically via the Galaxy Tool Shed is probably simplest.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	63
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	64
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	65 Manual Installation
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	66 ===================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	67
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	68 Normally you would install this via the Galaxy ToolShed, which would move
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	69 the provided ``blast.py`` file into a suitable location and process the
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	70 ``datatypes_conf.xml`` entries to be combined with your local configuration.
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	71
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	72 However, if you really want to this should work for a manual install. First
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	73 update the ``datatypes_conf.xml`` file in the Galaxy main folder by inserting
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	74 the contents of the ``<registration>`` and ``<sniffers>`` sections from the
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	75 small ``datatypes_conf.xml`` file provided in the tar-ball.
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	76
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	77 For the ``<registration>`` section you would add several ``<datatype ... />``
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	78 lines, one per new datatype::
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	79
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	80 <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/>
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	81 ...
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	82
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	83 Similarly, some of the new dataypes have ``<sniffer ... />`` lines used to
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	84 automatically recognise the datatype when uploaded into Galaxy::
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	85
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	86 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	87 ...
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	88
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	89 Also create the file ``lib/galaxy/datatypes/blast.py`` by moving, copying or linking
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	90 the ``blast.py`` file provided in this tar-ball. Finally add ``import blast`` near
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	91 the start of file ``lib/galaxy/datatypes/registry.py`` (after the other import
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	92 lines).
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	93
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	94
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	95 Bug Reports
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	96 ===========
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	97
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	98 You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	99 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	100
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	101
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	102 Developers
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	103 ==========
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	104
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	105 These BLAST+ datatypes and associated tools were originally developed on the
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	106 following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	107
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	108 As of July 2013, development is continuing on a dedicated GitHub repository:
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	109 https://github.com/peterjc/galaxy_blast
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	110
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	111 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	112 the following command from the ``blast_datatypes`` folder::
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	113
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	114 $ tar -czf blast_datatypes.tar.gz README.rst datatypes_conf.xml blast.py
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	115
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	116 Check this worked::
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	117
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	118 $ tar -tzf blast_datatypes.tar.gz
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	119 README.rst
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	120 datatypes_conf.xml
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	121 blast.py
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	122
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	123 For development, rather than having a local ToolShed running, I currently
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	124 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	125 described above.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	126
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	127
12 da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	128 Citation
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	129 ========
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	130
13 e96b515847dd v0.0.21 - Updated citation information with GigaScience paper peterjc parents: 12 diff changeset	131 Please cite the following paper:
12 da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	132
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	133 NCBI BLAST+ integrated into Galaxy.
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	134 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
13 e96b515847dd v0.0.21 - Updated citation information with GigaScience paper peterjc parents: 12 diff changeset	135 GigaScience 2015, 4:39
16 63befb860c3e planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes/ commit 1b9ec80b23b7fc9d3ed95afba3bc3b57dc3f47c2-dirty peterjc parents: 14 diff changeset	136 https://doi.org/10.1186/s13742-015-0080-7
12 da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	137
da92fef90117 Uploaded v0.0.20 with new citation information peterjc parents: 11 diff changeset	138
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	139 Licence (MIT)
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	140 =============
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	141
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	142 Permission is hereby granted, free of charge, to any person obtaining a copy
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	143 of this software and associated documentation files (the "Software"), to deal
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	144 in the Software without restriction, including without limitation the rights
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	145 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	146 copies of the Software, and to permit persons to whom the Software is
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	147 furnished to do so, subject to the following conditions:
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	148
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	149 The above copyright notice and this permission notice shall be included in
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	150 all copies or substantial portions of the Software.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	151
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	152 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	153 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	154 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	155 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	156 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	157 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	158 THE SOFTWARE.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	159
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	160 NOTE: This is the licence for the Galaxy BLAST datatypes only. BLAST+
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	161 and associated data files are available and licenced separately.

Mercurial > repos > devteam > blast_datatypes

annotate README.rst @ 19:db2480de852e draft default tip