Hello, I'm following "Managed Tool Dependencies" to the letter and still can't get Galaxy to find the executable. Is this page https://wiki.galaxyproject.org/Admin/Config/ToolDependencies up to date? If yes, what am I doing wrong? Any help greatly appreciated! # universe_wsgi.ini # I also tried the absolute path, it made no difference tool_dependency_dir = tool_dependencies # tool_dependencies is set like instructed: $ ls tool_dependencies/hhsuite/ 2.0.16/ default@ $ ls tool_dependencies/hhsuite/2.0.16/bin ffindex_build* ffindex_get* hhalign* hhblits* hhconsensus* hhfilter* hhmake* hhsearch* My tool: <tool id="hhpred_hhblits_01" name="Create MSA from single fasta for hhsearch" hidden="false" version="1.0.0" force_history_refresh="true"> <requirement type="package">hhsuite</requirement> <description>Searches single fasta iteratively against hmm db to build a MSA</description> <command>hhblits -i $input_file -d $database -oa3m $outfile</command> etc... Galaxy throws Error: hhblits not found. I've tried setting the PATH in the tool_dependencies/hhsuite/2.0.16/env.sh: #!/bin/bash # configure PATH to hhsuite binaries PATH="/opt/galaxy-dist/tool_dependencies/hhsuite/default/bin:$PATH" export PATH still getting hhblits not found :-( What am I doing wrong? Isabelle