Mercurial > repos > jankanis > blast2html
changeset 58:39df29f647e8
set other environment variables as well
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Tue, 27 May 2014 12:45:50 +0200 |
| parents | 159989f6bfa6 |
| children | f611cf649c90 |
| files | blast2html.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/blast2html.xml Mon May 26 15:34:54 2014 +0200 +++ b/blast2html.xml Tue May 27 12:45:50 2014 +0200 @@ -3,8 +3,6 @@ <description>Convert BLAST XML to HTML</description> <requirements> - <requirement type="package" version="v0.0.18">blast_datatypes</requirement> - <requirement name="package" version="3.4.1">python3</requirement> <requirement name="package" version="0.1">blast2html_venv</requirement> </requirements>
--- a/tool_dependencies.xml Mon May 26 15:34:54 2014 +0200 +++ b/tool_dependencies.xml Tue May 27 12:45:50 2014 +0200 @@ -39,12 +39,15 @@ # from within a virtual environment. unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME pyvenv blast2html_venv - . blast2html_venv/bin/activate - pip3 install lxml jinja2 + blast2html_venv/bin/pip3 install lxml jinja2 </action> <action type="set_environment"> - <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python3.4/site-packages</environment_variable> + <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment --> + <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/blast2html_venv/lib/python3.4/site-packages</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/blast2html_venv/bin</environment_variable> + <environment_variable name="PYTHONHOME" action="set_to"></environment_variable> + <!-- To find shared libraries such as libssl or libxml2 --> <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable> </action> </actions>