diff README.rst @ 27:b5e43dfe07ac draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit e4cd2df591ac5b9da5a1731e81f921313ed9e979

--- a/README.rst	Thu Aug 30 08:41:11 2018 -0400
+++ b/README.rst	Fri Sep 28 11:28:17 2018 -0400
@@ -29,8 +29,12 @@
 1. Install the dependencies
 ---------------------------
 
-The ``install_tool_deps.sh`` script can be used to fetch and install the
-dependencies locally, for example::
+If the tool is installed from the Galaxy toolshed (recommended) then
+the dependencies should be installed automatically and this step can
+be skipped.
+
+Otherwise the ``install_tool_deps.sh`` script can be used to fetch and
+install the dependencies locally, for example::
 
     install_tool_deps.sh /path/to/local_tool_dependencies
 
@@ -38,6 +42,8 @@
 created a set of directories containing the dependencies under the
 specified top level directory.
 
+*NB ``install_tool_deps.sh`` is no longer being maintained*
+
 2. Install the tool files
 -------------------------
 
@@ -203,9 +209,11 @@
 
 The following dependencies are currently unavailable:
 
- - fasta_number (need 02jun2015)
+ - R 3.2.1 (installed from the toolshed as the bioconda version
+   has conflicts )
  - microbiomeutil (need r20110519)
 
+
 (NB usearch 6.1.544 and 8.0.1623 are special cases which must be
 handled outside of Galaxy's dependency management systems.)
 
@@ -215,7 +223,8 @@
 ========== ======================================================================
 Version    Changes
 ---------- ----------------------------------------------------------------------
-1.2.2.1    Update to get dependencies from bioconda
+1.2.3.0    Updated to Amplicon_Analysis_Pipeline version 1.2.3; install
+           dependencies from bioconda and via tool_dependencies.xml
 1.2.2.0    Updated to Amplicon_Analysis_Pipeline version 1.2.2 (removes
            jackknifed analysis which is not captured by Galaxy tool)
 1.2.1.0    Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds