Mercurial > repos > peterjc > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_blast_plus.txt @ 2:b70b142bbc39 draft
Uploaded v0.0.16
author | peterjc |
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date | Wed, 17 Apr 2013 09:44:44 -0400 |
parents | c84837116457 |
children | cf4903f5c81f |
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Galaxy wrappers for NCBI BLAST+ suite ===================================== These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall). Note that these wrappers (and the associated datetypes) were originally distributed as part of the main Galaxy repository, but as of August 2012 moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). My thanks to Dannon Baker from the Galaxy development team for his assistance with this. Automated Installation ====================== Galaxy should be able to automatically install the dependencies, i.e. the 'blast_datatypes' repository which defines the BLAST XML file format ('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and 'blastdbn'). You must tell Galaxy about any system level BLAST databases using configuration files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein databases like NR), located in the tool-data folder. Sample fils are included which explain the tab based format to use. Manual Installation =================== For those not using Galaxy's automated installation from the Tool Shed, put the XML and Python files under tools/ncbi_blast_plus and add the XML files to your tool_conf.xml as normal. You will also need to install 'blast_datatypes' from the Tool Shed. This defines the BLAST XML file format ('blastxml') and protein and nucleotide BLAST databases composite file formats ('blastdbp' and 'blastdbn'). You must tell Galaxy about any system level BLAST databases using configuration files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein databases like NR), located in the tool-data folder. Sample fils are included which explain the tab based format to use. History ======= v0.0.11 - Final revision as part of the Galaxy main repository, and the first release via the Tool Shed v0.0.12 - Implements genetic code option for translation searches. - Changes <parallelism> to 1000 sequences at a time (to cope with very large sets of queries where BLAST+ can become memory hungry) - Include warning that BLAST+ with subject FASTA gives pairwise e-values v0.0.13 - Use the new error handling options in Galaxy (the previously bundled hide_stderr.py script is no longer needed). v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases in the history (using work from Edward Kirton), requires v0.0.14 of the 'blast_datatypes' repository from the Tool Shed. v0.0.15 - Stronger warning in help text against searching against subject FASTA files (better looking e-values than you might be expecting). v0.0.16 - Added repository_dependencies.xml for automates installation of the 'blast_datatypes' repository from the Tool Shed. Developers ========== This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use the following command from the Galaxy root folder: $ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh This similifies ensuring a consistent set of files is bundled each time, including all the relevant test files. 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 Wrapper only. NCBI BLAST+ and associated data files are available and licenced separately.