aahh, that must be it, thanks Bjoern! I have the symbolic link, but I did not have the 'requirements' section correct. thanks so much for your help, Isabelle On 6/5/14 9:27 AM, "Björn Grüning" <bjoern.gruening@gmail.com> wrote:

Hi Isabelle,

can you show us the "requirements" section from your tool? Also you need to have a symbolic link from tool_dependency_dir/hhsuite/2.0.16/ ponting to tool_dependency_dir/hhsuite/default/

In tool_dependency_dir/hhsuite/default/ should be the env.sh file. If you have the correct "requirements" section in your tool it should work.

Good luck! Bjoern

Am 04.06.2014 01:17, schrieb Isabelle Phan:

...

I am using env.sh to manage my tool dependencies:

# tool_dependency_dir/hhsuite/2.0.16/env.sh export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default export HHLIB=${HHPRED_DIR}/lib/hh export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH

Galaxy is not sourcing it. I have to manually source it before I restart Galaxy.

I am following "Using the env.sh file" and cannot get it to work. What am I missing?

Any help greatly appreciated,

thanks,

Isabelle

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