Mercurial > repos > peterjc > ncbi_blast_plus
changeset 9:b2eb4f48122f draft
Uploaded v0.0.19, adding FTP URLs to docs
| author | peterjc |
|---|---|
| date | Thu, 25 Apr 2013 09:36:38 -0400 |
| parents | e710b9446493 |
| children | e73da4ffaa6a |
| files | tool-data/blastdb.loc.sample tool-data/blastdb_p.loc.sample tools/ncbi_blast_plus/ncbi_blast_plus.txt |
| diffstat | 3 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/tool-data/blastdb.loc.sample Thu Apr 25 09:27:16 2013 -0400 +++ b/tool-data/blastdb.loc.sample Thu Apr 25 09:36:38 2013 -0400 @@ -30,10 +30,10 @@ #test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # +#You can download the NCBI provided protein databases like NT from here: +#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# #See also blastdb_p.loc which is for any protein BLAST database, and #blastdb_d.loc which is for any protein domains databases (like CDD). -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. -# + +
--- a/tool-data/blastdb_p.loc.sample Thu Apr 25 09:27:16 2013 -0400 +++ b/tool-data/blastdb_p.loc.sample Thu Apr 25 09:36:38 2013 -0400 @@ -23,5 +23,8 @@ #nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr #...etc... # +#You can download the NCBI provided protein databases like NR from here: +#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# #See also blastdb.loc which is for any nucleotide BLAST database, and #blastdb_d.loc which is for any protein domains databases (like CDD).
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:27:16 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:36:38 2013 -0400 @@ -6,7 +6,7 @@ See the licence text below. Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), -and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall). +and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). Note that these wrappers (and the associated datatypes) were originally distributed as part of the main Galaxy repository, but as of August 2012 @@ -25,9 +25,14 @@ You must tell Galaxy about any system level BLAST databases using configuration files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein -databases like NR), located in the tool-data/ folder. Sample files are included +databases like NR), and blastdb_d.loc (protein domain databases like CDD or +SMART) which are located in the tool-data/ folder. Sample files are included which explain the tab-based format to use. +You can download the NCBI provided databases as tar-balls from here: +ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) +ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) + Manual Installation =================== @@ -55,10 +60,8 @@ defines the BLAST XML file format ('blastxml') and protein and nucleotide BLAST databases composite file formats ('blastdbp' and 'blastdbn'). -You must tell Galaxy about any system level BLAST databases using configuration -files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein -databases like NR), located in the tool-data/ folder. Sample files are included -which explain the tab-based format to use. +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. You must install the NCBI BLAST+ standalone tools somewhere on the system path. Currently the unit tests are written using "BLAST 2.2.26+".