Hi,
can you try:
<requirements>
<requirement type="package">hhsuite</requirement>
</requirements>
Hope that helps, sorry for the short answer I'm too tired :)
Bjoern
Am 31.05.2014 01:53, schrieb Isabelle Phan:
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
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