diff tools/ncbi_blast_plus/ncbi_blast_plus.txt @ 8:1f546099212f draft

Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.

--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Fri Feb 08 05:51:26 2013 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt	Tue Feb 19 12:49:43 2013 -0500
@@ -34,7 +34,20 @@
 
 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.
+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">
+    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
+    <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
+    <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/blastxml_to_tabular.xml" />
+  </section>
 
 You will also need to install 'blast_datatypes' from the Tool Shed. This
 defines the BLAST XML file format ('blastxml') and protein and nucleotide
@@ -45,6 +58,14 @@
 databases like NR), located in the tool-data folder. Sample fils are included
 which explain the tab based format to use.
 
+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
+tool_conf.xml.sample file):
+
+./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
+
 
 History
 =======
@@ -65,6 +86,9 @@
           FASTA files (better looking e-values than you might be expecting).
 v0.0.16 - Added repository_dependencies.xml for automates installation of the
           'blast_datatypes' repository from the Tool Shed.
+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)
 
 
 Developers