| Previous changeset 1:165f0b05fa25 (2015-03-30) |
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Commit message:
Uploaded with note about NR versioning |
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modified:
README.rst |
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| diff -r 165f0b05fa25 -r db0c1bb92308 README.rst --- a/README.rst Mon Mar 30 11:34:25 2015 -0400 +++ b/README.rst Mon Mar 30 11:45:50 2015 -0400 |
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| @@ -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 ============ |