Mercurial > repos > peterjc > blast_rbh
view tools/blast_rbh/README.rst @ 18:f3ec931988fd draft
Uploaded 0.1.6c with the preprint citation (forgot to update source folder before making tar ball).
| author | peterjc |
|---|---|
| date | Tue, 27 Jan 2015 05:23:03 -0500 |
| parents | f26007c12312 |
| children | e8f8c580bcca |
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Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper ========================================================== This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. This tool is a short Python script to run reciprocal BLAST searches on a pair of sequence files, and extract the reciprocal best hits. The script ``blast_rbh.py`` can be used directly (without Galaxy) as long as NCBI BLAST+ is installed. It comes with an optional Galaxy tool definition file ``blast_rbh.xml`` allowing the Python script to be run from within Galaxy. It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Citation ======== Please cite the following paper (currently available as a preprint): NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) You should also cite the NCBI BLAST+ tools: BLAST+: architecture and applications. C. Camacho et al. BMC Bioinformatics 2009, 10:421. DOI: http://dx.doi.org/10.1186/1471-2105-10-421 Automated Installation ====================== Installation via the Galaxy Tool Shed should take care of the Galaxy side of things, including the dependency the NCBI BLAST+ binaries. Manual Installation =================== There are just two files to install: - ``blast_rbh.py`` (the Python script) - ``blast_rbh.xml`` (the Galaxy tool definition) The suggested location is in a ``tools/blast_rbh/`` folder. You will then need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding the line:: <tool file="blast_rbh/blast_rbh.xml" /> If you want to run the functional tests, copy the sample test files under sample test files under Galaxy's ``test-data/`` directory. Then:: ./run_tests.sh -id blast_reciprocal_best_hits You will need to have the NCBI BLAST+ binaries installed and on the ``$PATH``. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.1.0 - Initial Test Tool Shed release, targetting NCBI BLAST+ 2.2.29 v0.1.1 - Supports self-comparison, sometimes useful for spotting duplicates. v0.1.2 - Using optparse for command line API. - Tool definition now embeds citation information. - Fixed Tool Shed dependency definition. v0.1.3 - Option to make FASTA files non-redundant (via Biopython dependency). - Avoid extra database and BLAST search in self-comparison mode. v0.1.4 - Check for duplicate FASTA identifiers (workaround for makeblastdb not treating this as an error, leading to confusing RBH output). v0.1.5 - Clarify documentation for using the Python script outside Galaxy. - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install. v0.1.6 - Offer the new blastp-fast task added in BLAST+ 2.2.30. - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. ======= ====================================================================== Developers ========== This tool is developed on the following GitHub repository: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use the following command from the Galaxy root folder:: $ tar -czf blast_rbh.tar.gz tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/blast_rbh.py tools/blast_rbh/tool_dependencies.xml test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta test-data/four_human_proteins.fasta test-data/k12_edited_proteins.fasta test-data/k12_ten_proteins.fasta test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_none.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular Check this worked:: $ tar -tzf blast_rbh.tar.gz tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/blast_rbh.py tools/blast_rbh/tool_dependencies.xml test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta test-data/four_human_proteins.fasta test-data/k12_edited_proteins.fasta test-data/k12_ten_proteins.fasta test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_none.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular 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.