--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/README	Tue Jun 07 18:03:34 2011 -0400
@@ -0,0 +1,59 @@
+This package contains Galaxy wrappers for two standalone command line protein
+analysis tools (SignalP 3.0 and THMHMM 2.0) from the Center for Biological
+Sequence Analysis at the Technical University of Denmark,
+http://www.cbs.dtu.dk/cbs/
+
+To use these Galaxy wrappers you must first install the CBS command line
+tools. At the time of writing both SignalP 3.0 and TMHMM 2.0 are free for
+academic use.
+
+These wrappers are copyright 2010 by Peter Cock, SCRI, UK. All rights
+reserved. See the included LICENCE file for details.
+
+Installation
+============
+
+1. Install the command line version of SignalP 3.0 and ensure it is on the
+   PATH, see: http://www.cbs.dtu.dk/services/SignalP/
+
+2. Install the command line version of TMHMM 2.0 and ensure it is on the
+   PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
+
+3. Create a folder tools/protein_analysis under your Galaxy installation.
+
+4. Copy/move the following files (from this archive) there:
+
+tmhmm2.xml (Galaxy tool definition)
+tmhmm2.py (Python wrapper script)
+signalp3.xml (Galaxy tool definition)
+signalp3.py (Python wrapper script)
+seq_analysis_utils.py (shared Python code)
+README (optional)
+
+5. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
+   also tool_conf.xml.sample (to run the tests) to include the two new tools
+   by adding:
+
+  <section name="Protein sequence analysis" id="protein_analysis">
+    <tool file="protein_analysis/tmhmm2.xml" />
+    <tool file="protein_analysis/signalp3.xml" />
+  </section>
+
+6. Copy/move the following test files (from these archive) to Galaxy
+   subfolder test-data:
+
+four_human_proteins.fasta
+four_human_proteins.signalp3.tsv
+four_human_proteins.tmhmm2.tsv
+
+7. Run the Galaxy functional tests for these new wrappers with:
+
+./run_functional_tests.sh -id tmhmm2
+./run_functional_tests.sh -id signalp3
+
+Alternatively, this should work (assuming you left the name and id as shown in
+the XML file tool_conf.xml.sample):
+
+./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
+
+8. Restart Galaxy and check the new tools are shown and work.