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:
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.