Not sure about specifying the absolute path for the tool dependency dir, but I
always use it. Also, my env.sh neither has a #!/bin/bash shebang line, nor
quote marks around the tool path.
If you are in the hhsuite/default/ dir and source env.sh, can you then run
hhblits yourself (as galaxy user, or whoever owns the tools)?
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
On 31 May 2014, at 01:53, Isabelle Phan <isabelle.p...@seattlebiomed.org> wrote:
> 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
> <command>hhblits -i $input_file -d $database -oa3m $outfile</command>
> Galaxy throws Error: hhblits not found.
> I've tried setting the PATH in the tool_dependencies/hhsuite/2.0.16/env.sh:
> # configure PATH to hhsuite binaries
> export PATH
> still getting hhblits not found :-(
> What am I doing wrong?
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