Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/README.rst @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
| author | peterjc |
|---|---|
| date | Sun, 05 Jul 2015 10:37:27 -0400 |
| parents | 2fe07f50a41e |
| children | b5f1f599d1fb |
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--- a/tools/ncbi_blast_plus/README.rst Mon Dec 01 05:59:16 2014 -0500 +++ b/tools/ncbi_blast_plus/README.rst Sun Jul 05 10:37:27 2015 -0400 @@ -7,7 +7,7 @@ See the licence text below. -Currently tested with NCBI BLAST 2.2.29+ (i.e. version 2.2.29 of BLAST+), +Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+), and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). Note that these wrappers (and the associated datatypes) were originally @@ -19,6 +19,25 @@ 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 (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 ====================== @@ -35,8 +54,7 @@ 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 (and do the same in -``tool_conf.xml.sample`` in order to run the unit tests). For example, use:: +XML files to your ``tool_conf.xml`` as normal. For example, use:: <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> @@ -61,15 +79,16 @@ 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. +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 2.2.29+. +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_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools + ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools Configuration ============= @@ -157,7 +176,7 @@ - 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. + - 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. @@ -170,8 +189,8 @@ - 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. + - 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). @@ -181,6 +200,21 @@ 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). ======= ====================================================================== @@ -201,10 +235,28 @@ As of July 2013, development is continuing on a dedicated GitHub repository: https://github.com/peterjc/galaxy_blast -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use -the following command from the GitHub repository root folder:: +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 --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ + ... + +or:: - $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/ncbi_blast_plus/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/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.