Mercurial > repos > peterjc > blast_top_hit_species

changeset 2:db0c1bb92308 draft default tip

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Uploaded with note about NR versioning
author peterjc
date Mon, 30 Mar 2015 11:45:50 -0400
parents 165f0b05fa25
children
files README.rst
diffstat 1 files changed, 19 insertions(+), 0 deletions(-) [+]
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--- a/README.rst	Mon Mar 30 11:34:25 2015 -0400
+++ b/README.rst	Mon Mar 30 11:45:50 2015 -0400
@@ -98,6 +98,9 @@
 Known Issues
 ============
 
+Counts
+------
+
 This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with
 the current stable release (Galaxy v15.03, i.e. March 2015).
 
@@ -114,6 +117,22 @@
 this is included in the next stable Galaxy release - or migrated to the
 Galaxy Tool Shed.
 
+NCBI nr database
+----------------
+
+The use of external datasets within Galaxy via the ``*.loc`` configuration
+files undermines provenance tracking within Galaxy. This is exacerbated
+by the lack of officially versioned BLAST database releases by the NCBI.
+
+This workflow assumes that you have an entry ``nr`` in your ``blastdb_p.loc``
+(the configuration file listing locally installed BLAST databases external
+to Galaxy - consult the NCBI BLAST+ wrapper documentation for more details),
+and that this points to a mirror of the latest NCBI "non-redundant" database
+from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
+
+i.e. The workflow is intended to be used against the *latest* nr database,
+and thus is not reproducible over the long term as the database changes.
+
 
 Availability
 ============