diff tools/ncbi_blast_plus/ncbi_blast_plus.txt @ 9:9dabbfd73c8a draft

Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database. Also includes other minor improvements.

--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Tue Feb 19 12:49:43 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Thu Apr 25 09:38:37 2013 -0400
@@ -6,9 +6,9 @@
 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 datetypes) were originally
+Note that these wrappers (and the associated datatypes) were originally
 distributed as part of the main Galaxy repository, but as of August 2012
 moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes').
 My thanks to Dannon Baker from the Galaxy development team for his assistance
@@ -25,16 +25,21 @@
 
 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 fils are included
-which explain the tab based format to use.
+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
 ===================
 
 For those not using Galaxy's automated installation from the Tool Shed, put
-the XML and Python files under tools/ncbi_blast_plus and add the XML files
-to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample
+the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML
+files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample
 in order to run the unit tests). For example, use:
 
   <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
@@ -46,6 +51,8 @@
     <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" />
     <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" />
     <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" />
+    <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" />
     <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
   </section>
 
@@ -53,15 +60,13 @@
 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 fils 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+".
 
-Run the functional tests (adusting the section identifier to match your
+Run the functional tests (adjusting the section identifier to match your
 tool_conf.xml.sample file):
 
 ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
@@ -89,20 +94,28 @@
 v0.0.17 - The BLAST+ search tools now default to extended tabular output
           (all too often our users where having to re-run searches just to
           get one of the missing columns like query or subject length)
+v0.0.18 - Defensive quoting of filenames in case of spaces (where possible,
+          BLAST+ handling of some mult-file arguments is problematic).
+v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc
+          for the domain databases they use (e.g. CDD, PFAM or SMART).
+        - Correct case of exception regular expression (for error handling
+          fall-back in case the return code is not set properly).
+        - Clearer naming of output files.
 
 
 Developers
 ==========
 
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
+This script and related tools are being developed on the 'tools' branch of the
+following Mercurial repository:
+https://bitbucket.org/peterjc/galaxy-central/
 
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
 the following command from the Galaxy root folder:
 
 $ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh
 
-This similifies ensuring a consistent set of files is bundled each time,
+This simplifies ensuring a consistent set of files is bundled each time,
 including all the relevant test files.