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comparison README.rst @ 12:da92fef90117 draft

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Uploaded v0.0.20 with new citation information
author peterjc
date Wed, 25 Feb 2015 10:50:44 -0500
parents 236046d1d441
children e96b515847dd
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11:236046d1d441 12:da92fef90117
39 - Nucleotide database definition aware of MegaBLAST index superheader 39 - Nucleotide database definition aware of MegaBLAST index superheader
40 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes 40 v0.0.17 - Add ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` sub-datatypes
41 (contribution from Nicola Soranzo) 41 (contribution from Nicola Soranzo)
42 v0.0.18 - Add retries to BLAST XML merge code. 42 v0.0.18 - Add retries to BLAST XML merge code.
43 - Modify display_data method to allow unit tests to function. 43 - Modify display_data method to allow unit tests to function.
44 v0.0.19 - Add ``blastdbp`` datatype for BLAST protein domain databases, for use 44 v0.0.19 - Add ``blastdbd`` datatype for BLAST protein domain databases, for use
45 with makeprofiledb and rpsblast (contribution from Bjoern Gruening). 45 with makeprofiledb and rpsblast (contribution from Bjoern Gruening).
46 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices 46 - Add ``pssm-asn1`` datatype for Position Specific Scoring Matrices
47 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named 47 (PSSMs) stored in NCBI's "scoremat" ASN.1 format (usually named
48 as *.smp), used as input files for makeprofiledb. 48 as ``*.smp``), used as input files for makeprofiledb.
49 v0.0.20 - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
49 ======= ====================================================================== 50 ======= ======================================================================
50 51
51 52
52 Installation 53 Installation
53 ============ 54 ============
116 For development, rather than having a local ToolShed running, I currently 117 For development, rather than having a local ToolShed running, I currently
117 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as 118 use a symlink from ``lib/galaxy/datatypes/blast.py`` to the actual file as
118 described above. 119 described above.
119 120
120 121
122 Citation
123 ========
124
125 Please cite the following paper (currently available as a preprint):
126
127 NCBI BLAST+ integrated into Galaxy.
128 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
129 bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
130
131
121 Licence (MIT) 132 Licence (MIT)
122 ============= 133 =============
123 134
124 Permission is hereby granted, free of charge, to any person obtaining a copy 135 Permission is hereby granted, free of charge, to any person obtaining a copy
125 of this software and associated documentation files (the "Software"), to deal 136 of this software and associated documentation files (the "Software"), to deal