Re: [galaxy-dev] galaxy is not sourcing tool environment

2014-06-05 Thread Björn Grüning
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

Re: [galaxy-dev] galaxy is not sourcing tool environment

2014-06-05 Thread Isabelle Phan
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.gruen...@gmail.com wrote: Hi Isabelle, can you show us the requirements section from your

[galaxy-dev] galaxy is not sourcing tool environment

2014-06-03 Thread 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