changeset 3:a66c358bfbcf draft

Uploaded with README clarifications

--- a/README.rst	Mon Mar 30 11:35:12 2015 -0400
+++ b/README.rst	Wed Apr 08 06:06:30 2015 -0400
@@ -98,22 +98,46 @@
 Known Issues
 ============
 
-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).
+Counts
+------
 
-The updated "Count" tool version 1.0.1 includes a fix not to remove spaces
+This workflow uses the Galaxy "Count" tool (tool id ``Count1``) version
+1.0.0, as shipped with the current stable release (Galaxy v15.03, i.e.
+March 2015).
+
+The updated "Count" tool version 1.0.1 included a fix not to remove spaces
 in the fields being counted. In the example above, while the top hits are
 not affected, minor entries like "cellular slime molds" are shown as
-"cellularslimemolds" instead (look closely at the Pie Chart key)..
+"cellularslimemolds" instead (look closely at the Pie Chart key).
 
-The updated "Count" tool version 1.0.1 also adds a new option to sort the
-output, which avoids the additional sorting step in the current version of
-the workflow.
+The updated "Count" tool version 1.0.2 added a new option to sort the
+output, which would allow skipping the final sorting step in the current
+version of this workflow.
 
 A future update to this workflow will use the revised "Count" tool, once
 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.
+
+Note that if your ``blastdb_p.loc`` is missing an entry ``nr`` then the
+workflow should abort. However as of Galaxy v15.03 (March 2015) there is
+a problem with how this is handled: https://trello.com/c/lkYlW14W/
+
 
 Availability
 ============
@@ -175,11 +199,11 @@
 
 https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species
 
-To prepare the tar-ball for uploading to the Tool Shed, I use this:
+To prepare the tar-ball for uploading to the Tool Shed, I use this::
 
     $ tar -cf blast_top_hit_species.tar.gz README.rst repository_dependencies.xml blast_top_hit_species.ga blast_top_hit_species.png N_abberans_piechart_mouseover.png
 
-Check this,
+Check this::
 
     $ tar -tzf blast_top_hit_species.tar.gz
     README.rst

--- a/repository_dependencies.xml	Mon Mar 30 11:35:12 2015 -0400
+++ b/repository_dependencies.xml	Wed Apr 08 06:06:30 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <repositories description="This workflow requires the NCBI BLAST+ tools etc">
-    <repository changeset_revision="5e9d5e536b79" name="ncbi_blast_plus" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="6119ddccd8a3" name="ncbi_blast_plus" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="ae709fd50581" name="fasta_to_tabular" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="4231c585b6dd" name="sample_seqs" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="2064ae2602b1" name="unique" owner="bgruening" toolshed="https://testtoolshed.g2.bx.psu.edu" />