Mercurial > repos > peterjc > blast_top_hit_species

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Uploaded with note about NR versioning
author peterjc
date Mon, 30 Mar 2015 11:45:50 -0400
parents 165f0b05fa25
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1:165f0b05fa25 2:db0c1bb92308
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98 Known Issues 98 Known Issues
99 ============ 99 ============
100 100
101 Counts
102 ------
103
101 This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with 104 This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with
102 the current stable release (Galaxy v15.03, i.e. March 2015). 105 the current stable release (Galaxy v15.03, i.e. March 2015).
103 106
104 The updated "Count" tool version 1.0.1 includes a fix not to remove spaces 107 The updated "Count" tool version 1.0.1 includes a fix not to remove spaces
105 in the fields being counted. In the example above, while the top hits are 108 in the fields being counted. In the example above, while the top hits are
111 the workflow. 114 the workflow.
112 115
113 A future update to this workflow will use the revised "Count" tool, once 116 A future update to this workflow will use the revised "Count" tool, once
114 this is included in the next stable Galaxy release - or migrated to the 117 this is included in the next stable Galaxy release - or migrated to the
115 Galaxy Tool Shed. 118 Galaxy Tool Shed.
119
120 NCBI nr database
121 ----------------
122
123 The use of external datasets within Galaxy via the ``*.loc`` configuration
124 files undermines provenance tracking within Galaxy. This is exacerbated
125 by the lack of officially versioned BLAST database releases by the NCBI.
126
127 This workflow assumes that you have an entry ``nr`` in your ``blastdb_p.loc``
128 (the configuration file listing locally installed BLAST databases external
129 to Galaxy - consult the NCBI BLAST+ wrapper documentation for more details),
130 and that this points to a mirror of the latest NCBI "non-redundant" database
131 from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
132
133 i.e. The workflow is intended to be used against the *latest* nr database,
134 and thus is not reproducible over the long term as the database changes.
116 135
117 136
118 Availability 137 Availability
119 ============ 138 ============
120 139