| Previous changeset 84:4340432b7191 (2014-06-24) Next changeset 89:8a712d393559 (2014-06-24) |
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Commit message:
merge py2.6 branch |
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modified:
blast2html.xml tool_dependencies.xml |
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| diff -r 4340432b7191 -r 24deecb59ce9 blast2html.xml --- a/blast2html.xml Tue Jun 24 11:00:57 2014 +0200 +++ b/blast2html.xml Tue Jun 24 16:49:05 2014 +0200 |
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| @@ -1,12 +1,12 @@ -<tool id="blast2html" name="blast2html" version="0.0.9"> +<tool id="blast2html" name="blast2html" version="0.0.10"> <description>Convert BLAST XML to HTML</description> <requirements> - <requirement name="package" version="0.1">blast2html_venv</requirement> + <requirement name="package" version="0.2">blast2html_venv</requirement> </requirements> - <command interpreter="python3">blast2html.py -i "${input}" -o "${output}"</command> + <command interpreter="python">blast2html.py -i "${input}" -o "${output}"</command> <stdio> <!-- Any exit code other than 0 is an error --> |
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| diff -r 4340432b7191 -r 24deecb59ce9 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 24 11:00:57 2014 +0200 +++ b/tool_dependencies.xml Tue Jun 24 16:49:05 2014 +0200 |
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| @@ -10,12 +10,7 @@ toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" /> </package> - <package name="python3" version="3.4.1"> - <repository name="package_python3_4" owner="jankanis" prior_installation_required="True" - toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="d30e6a97dfbf" /> - </package> - - <package name="blast2html_venv" version="0.1"> + <package name="blast2html_venv" version="0.2"> <install version="1.0"> <actions> <action type="set_environment_for_install"> @@ -27,34 +22,27 @@ toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee"> <package name="libxslt" version="1.1.28" /> </repository> - <repository name="package_python3_4" owner="jankanis" - toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="d30e6a97dfbf"> - <package name="python3" version="3.4.1" /> - </repository> </action> - - <action type="shell_command"> - # Unset any saved environment settings from parent virtual - # environments, e.g. for python 2 or if Galaxy itself is running - # from within a virtual environment. - unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME - pyvenv blast2html_venv - blast2html_venv/bin/pip3 install lxml jinja2 - </action> - + + <action type="setup_virtualenv"> + jinja2==2.7.3 + six==1.7.2 + argparse==1.2.1 + </action> + + <!-- install lxml manually, as the setup_virtualenv action does not include the environment + from set_environment_for_install but shell_command does --> + <action type="shell_command"> + $INSTALL_DIR/venv/bin/pip install lxml==3.3.5 + </action> + <action type="set_environment"> - <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment --> - <environment_variable name="PYTHONPATH" action="set_to">$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> - <!-- libxml2 doesn't actually export its own LD_LIBRARY_PATH --> + <!-- add libxml2 library path so the runtime can find the shared library --> <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LIBXML_ROOT_PATH]/lib</environment_variable> </action> </actions> </install> - <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme> + <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme> </package> </tool_dependency> |