blast_datatypes: README.rst annotate

annotate README.rst @ 10:939a600f45e9 draft

Uploaded v0.0.19, domain databases and PSSM

author	peterjc
date	Wed, 19 Mar 2014 10:51:02 -0400
parents	e36c60d13c94
children	236046d1d441

rev	line source
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	1 Galaxy datatypes for NCBI BLAST+ suite
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	2 ======================================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	3
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	4 These Galaxy datatypes are copyright 2010-2013 by Peter Cock, The James Hutton
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	5 Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	6 Contributions/revisions copyright 2012 Edward Kirton. All rights reserved.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	7 Contributions/revisions copyright 2013 Nicola Soranzo. All rights reserved.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	8
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	9 See the licence text below.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	10
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	11 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	12 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	13 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	14 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	15 assistance with this.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	16
8 7ceb2ae30ff4 Uploaded v0.0.17, Add maskinfo-asn1 and maskinfo-asn1-binary sub-datatypes peterjc parents: 7 diff changeset	17 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	18 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	19
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	20
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	21 History
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	22 =======
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 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	25 not used explicitly in the datatypes themselves.
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 ======= ======================================================================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	28 Version Changes
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 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	31 first release via the Tool Shed
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	32 v0.0.13 - Uses blast.py instead of xml.py to define the datatypes
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	33 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	34 (``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	35 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	36 BLAST database files (contribution from Nicola Soranzo)
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	37 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	38 - Use reStructuredText for this README file.
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	39 - 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	40 - Nucleotide database definition aware of MegaBLAST index superheader
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	41 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes
9 e36c60d13c94 Uploaded v0.0.18, tweak display_data for running tests peterjc parents: 8 diff changeset	42 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	43 - Modify display_data method to allow unit tests to function.
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	44 v0.0.19 - Add ``blastdbp`` datatype for BLAST protein domain databases, for use
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	45 with makeprofiledb and rpsblast (contribution from Bjoern Gruening).
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	46 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	47 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	48 as *.smp), used as input files for makeprofiledb.
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	49 ======= ======================================================================
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	50
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	51
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	52 Installation
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	53 ============
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	54
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	55 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	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 Manual Installation
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	59 ===================
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 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	62 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	63 ``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	64
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	65 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	66 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	67 the contents of the ``<registration>`` and ``<sniffers>`` sections from the
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	68 small ``datatypes_conf.xml`` file provided in the tar-ball.
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	69
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	70 For the ``<registration>`` section you would add several ``<datatype ... />``
939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	71 lines, one per new datatype::
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	72
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	73 <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	74 ...
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	75
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	76 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	77 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	78
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	79 <sniffer type="galaxy.datatypes.blast:BlastXml"/>
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	80 ...
6 8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	81
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	82 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	83 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	84 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	85 lines).
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	86
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	87
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	88 Bug Reports
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	89 ===========
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	90
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	91 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	92 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	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 Developers
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
10 939a600f45e9 Uploaded v0.0.19, domain databases and PSSM peterjc parents: 9 diff changeset	98 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	99 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	100
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	101 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	102 https://github.com/peterjc/galaxy_blast
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 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	105 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	106
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	107 $ 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	108
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	109 Check this worked::
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 $ tar -tzf blast_datatypes.tar.gz
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	112 README.rst
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	113 datatypes_conf.xml
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	114 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 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	117 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	118 described above.
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	119
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	120
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	121 Licence (MIT)
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
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	124 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	125 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	126 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	127 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	128 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	129 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	130
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	131 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	132 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	133
8615fd8abc04 Uploaded v0.0.16, moving to MIT license and development on GitHub. peterjc parents: diff changeset	134 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	135 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	136 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	137 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	138 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	139 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	140 THE SOFTWARE.
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 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	143 and associated data files are available and licenced separately.

Mercurial > repos > devteam > blast_datatypes

annotate README.rst @ 10:939a600f45e9 draft