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Repository ncbi_blast_plus
Owner: devteam
Synopsis: NCBI BLAST+
The NCBI BLAST+ tools find regions of similarity between biological sequences.
The programs compare nucleotide or protein sequences to sequence databases and
calculate the statistical significance.
Type: unrestricted
Revision: 26:2889433c7ae1
This revision can be installed: True
Times cloned / installed: 11378

Repository README files - may contain important installation or license information

Galaxy wrappers for NCBI BLAST+ suite ===================================== These wrappers are copyright 2010-2018 by Peter Cock (James Hutton Institute, UK) and additional contributors including Edward Kirton, John Chilton, Nicola Soranzo, Jim Johnson, Bjoern Gruening, Caleb Easterly, and Anton Nekrutenko. See the licence text below. Note this does not work with the NCBI 'legacy' BLAST suite written in C (e.g. binary name ``blastall``), but its replacement BLAST, which is written in C++ (e.g. binary name ``blastn``). Note that these wrappers (and the associated datatypes) 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. These wrappers are available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus In-development test releases are available from the Test Tool Shed at: http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ Citation ======== Please cite the following paper: NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo GigaScience, 2015, 4:39 https://doi.org/10.1186/s13742-015-0080-7 You should also cite the NCBI BLAST+ tools: BLAST+: architecture and applications. C. Camacho et al. BMC Bioinformatics 2009, 10:421. https://doi.org/10.1186/1471-2105-10-421 Automated Installation ====================== Galaxy should be able to automatically install the dependencies, i.e. the BLAST+ binaries and the ``blast_datatypes`` repository which defines the BLAST XML file format (``blastxml``), protein and nucleotide BLAST databases (``blastdbp`` and ``blastdbn``), and so on. See the configuration notes below. Manual Installation =================== For those not using Galaxy's automated installation from the Tool Shed, put the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the XML files to your ``tool_conf.xml`` as normal. For example, use::
You will also need to install ``blast_datatypes`` from the Tool Shed. This defines the BLAST XML file format (``blastxml``), BLAST databases, etc: * http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes As described above for an automated installation, you must also tell Galaxy about any system level BLAST databases using the ``tool-data/blastdb*.loc`` files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents into your ``tool_data_table_conf.xml`` file. You must install the NCBI BLAST+ standalone tools somewhere on the system path. Currently the unit tests are written using BLAST+ 2.2.30. Run the functional tests (adjusting the section identifier to match your ``tool_conf.xml.sample`` file):: ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools Configuration ============= 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), and ``blastdb_d.loc`` (protein domain databases like CDD or SMART) which are located in the ``tool-data/`` folder. Sample files are included which explain the tab-based format to use. You can download the NCBI provided databases as tar-balls from here: * ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) * ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) If using the optional taxonomy columns, you will also need to download the NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on the BLAST database FTP site). Currently explicit version tracking of the taxonomy is not supported, and in order to use this you must set the ``$BLASTDB`` environment variable to include the path where you unzipped the taxonomy files. If this is not done, the taxonomy columns like species name will appear as ``N/A`` in the tabular output. The BLAST+ binaries support multi-threaded operation, which is handled via the ``$GALAXY_SLOTS`` environment variable. This should be set automatically by Galaxy via your job runner settings, which allows you to (for example) allocate four cores to each BLAST job. In addition, the BLAST+ wrappers also support high level parallelism by task splitting if ``use_tasked_jobs = True`` is enabled in the ``config/galaxy.ini`` configuration file (previously ``universe_wsgi.ini`` on older versions of Galaxy). Essentially, the FASTA input query files are broken up into batches of 1000 sequences, a separate BLAST child job is run for each chunk, and then the BLAST output files are merged (in order). This is transparent for the end user. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- 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 ```` 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. v0.0.17 - The BLAST+ search tools now default to extended tabular output (all too often our users where having to re-run searches just to get one of the missing columns like query or subject length) v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, BLAST+ handling of some multi-file arguments is problematic). v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` for the domain databases they use (e.g. CDD, PFAM or SMART). - Correct case of exception regular expression (for error handling fall-back in case the return code is not set properly). - Clearer naming of output files. v0.0.20 - Added unit tests for BLASTN and TBLASTX. - Added percentage identity option to BLASTN. - Fallback on ElementTree if cElementTree missing in XML to tabular. - Link to Tool Shed added to help text and this documentation. - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed. - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. - Adopted standard MIT License. - Development moved to GitHub, https://github.com/peterjc/galaxy_blast - Updated citation information (Cock et al. 2013). v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). - Added wrapper for dustmasker. - Enabled masking for makeblastdb (Nicola Soranzo). - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. v0.0.22 - More use of macros to simplify the wrappers. - Set number of threads via ``$GALAXY_SLOTS`` environment variable. - More descriptive default output names. - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. - Extended tabular output includes 'salltitles' as column 25. v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. - Tabular output now includes option to pick specific columns (based on contribution from Jim Johnson), including previously unavailable taxonomy columns. - BLAST XML to tabular tool supports multiple input files (based on contribution from Jim Johnson). - More detailed descriptions for BLASTN and BLASTP task option. - Wrappers for segmasker, dustmasker and convert2blastmask (contribution from Bjoern Gruening). - Supports using maskinfo with ``makeblastdb`` wrapper. - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. - Subtle changes like new conditional settings will require some old workflows be updated to cope. v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). - Wrapper for makeprofiledb added to create protein domain databases (based on contribution from Bjoern Gruening). - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein domain database from the user's history. - Tool definitions now embed citation information (by John Chilton). - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. - New minimum query HSP coverage option, ``-qcov_hsp_perc``. - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this is set during database construction and should not have been offered as a command line option in releases prior to BLAST+ 2.2.30. - BLAST database ``blastdb*.loc`` files now accessed via the XML table definitions in Galaxy's ``tool_data_table_conf.xml`` file, setup via ``tool-data/tool_data_table_conf.xml.sample`` - Replace ``.extra_files_path`` with ``.files_path`` (internal change, thanks to Bjoern Gruening and John Chilton). - Added *"NCBI BLAST+ integrated into Galaxy"* preprint citation. v0.1.03 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.1.04 - Fixed regression using BLAST databases from the history. Currently Galaxy inputs must still use ``.extra_files_path`` rather than the more consise ``.extra_files`` available for output files (Issue #69) v0.1.05 - Define ``parallelism`` tag via a macro (internal change only). - Define wrapper versions via a macro (internal change only). - Update citation information now GigaScience paper is out. v0.1.06 - Now depends on ``package_blast_plus_2_2_31`` in ToolShed. - Tests updated for BLAST+ 2.2.31 instead of BLAST+ 2.2.30. v0.1.07 - Re-enabled some ``*.loc`` file tests (these had not been supported on the Tool Shed test framework, but that is not currently in use). - Fixed macro problem with version field in blastxml_to_tabular.xml (contribution from Bjoern Gruening and Daniel Blankenberg). v0.1.08 - Allow searching against multiple locally installed databases (contribution from Gildas Le Corguillé and Emma Prudent). - Minor XML and Python style changes (internal change only). - Set ``allow_duplicate_entries="False"`` in sample configuration file ``tool_data_table_conf.xml``. - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). v0.2.00 - Updated for NCBI BLAST+ 2.5.0, where GI numbers are less visible, tabular output changes with `-parse_deflines`, and percentage identifies are now given to 3dp rather than 2dp. - Depends on ``package_blast_plus_2_5_0`` in ToolShed, or BioConda. - ``blastxml_to_tabular`` now also gives percentage idenity to 3dp. - Removed never-used binary and Python module dependency declarations (internal change only). v0.2.01 - Use ```` (internal change only). - Single quote command line arguments (internal change only). - Show BLAST command line argument corresponding to each tool parameter (contribution from Nicola Soranzo). - Add ``-max_hsps`` option (contribution from Nicola Soranzo). - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo). v0.2.02 - Document the BLAST+ 2.5.0 change in the standard 12 column output from ``qseqid,sseqid,...`` to ``qacc,sacc,...`` instead. - Support for per-matrix recommended gaps settings (``-gapopen`` and ``-gapextend``, contribution from Caleb Easterly and Jim Johnson). - Support for ``-window_size``, ``-threshold``, ``-comp_based_stats`` and revising ``-word_size`` to avoid using zero to mean default (contribution from Caleb Easterly). v0.3.0 - Updated for NCBI BLAST+ 2.7.1, - Depends on BioConda or legacy ToolShed ``package_blast_plus_2_7_1``. - Document the BLAST+ 2.6.0 change in the standard 12 column output from ``qacc,sacc,...`` to ``qaccver,saccver,...`` instead. - Accept gzipped FASTA inputs for subject files, queries to ``blastn`` and input to ``makeblastdb`` (contribution from Anton Nekrutenko). v0.3.1 - Clarify help text for max hits option, confusing as depending on the output format it must be mapped to different command line arguments. - Extend gzipped query support to all the command line tools. - Workaround for gzipped support under Galaxy release 16.01 or older. v0.3.2 - Fixed incomplete ``@CLI_OPTIONS@`` macro in the help text for the ``tblastn`` and ``blastdbcmd`` wrappers. v0.3.3 - Fixed ``tool_dependencies.xml`` to use BLAST+ 2.7.1 (useful only for older Galaxy instances - we recommend conda for dependencies now). ======= ====================================================================== 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 ========== This script and related tools were originally developed on the 'tools' branch of the following Mercurial repository: https://bitbucket.org/peterjc/galaxy-central/ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_update -t testtoolshed --check_diff tools/ncbi_blast_plus/ ... or:: $ planemo shed_update -t toolshed --check_diff tools/ncbi_blast_plus/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only tools/ncbi_blast_plus/ ... $ tar -tzf shed_upload.tar.gz test-data/blastdb.loc ... tools/ncbi_blast_plus/tool_dependencies.xml $ tar -tzf shed_upload.tar.gz | wc -l 117 This simplifies ensuring a consistent set of files is bundled each time, including all the relevant test files. When updating the version of BLAST+, many of the sample data files used for the unit tests must be regenerated. This script automates that task:: $ tools/ncbi_blast_plus/update_test_files.sh 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.
Dependencies of this repository

Repository blast_datatypes revision 01b38f20197e owned by devteam
Repository package_blast_plus_2_7_1 revision 2e9109a8924f owned by iuc

Name Version Type
blast 2.7.1 package

Contents of this repository

Name Description Version Minimum Galaxy Version
Convert BLAST XML output to tabular 0.3.3 16.01
Show BLAST database information from blastdbcmd 0.3.3 16.01
Extract sequence(s) from BLAST database 0.3.3 16.01
Search nucleotide database with nucleotide query sequence(s) 0.3.3 16.01
Search protein database with protein query sequence(s) 0.3.3 16.01
Search protein database with translated nucleotide query sequence(s) 0.3.3 16.01
Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb 0.3.3 16.01
masks low complexity regions 0.3.3 16.01
Make BLAST database 0.3.3 16.01
Make profile database 0.3.3 16.01
Search protein domain database (PSSMs) with protein query sequence(s) 0.3.3 16.01
Search protein domain database (PSSMs) with translated nucleotide query sequence(s) 0.3.3 16.01
low-complexity regions in protein sequences 0.3.3 16.01
Search translated nucleotide database with protein query sequence(s) 0.3.3 16.01
Search translated nucleotide database with translated nucleotide query sequence(s) 0.3.3 16.01

Categories
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis