Mercurial > repos > bgruening > antismash
changeset 17:213d82f33fc2 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 11 Oct 2013 19:24:56 -0400 |
| parents | e2df6fe8b447 |
| children | c87f223b0ad9 |
| files | antismash.xml tool_dependencies.xml |
| diffstat | 2 files changed, 32 insertions(+), 9 deletions(-) [+] |
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--- a/antismash.xml Fri Oct 11 16:46:08 2013 -0400 +++ b/antismash.xml Fri Oct 11 19:24:56 2013 -0400 @@ -4,7 +4,8 @@ <requirement type="package" version="3.0">hmmer</requirement> <requirement type="package" version="2.2.28">blast+</requirement> <requirement type="package" version="3.8.31">muscle</requirement> - <requirement type="package" version="2.0.2">antismash_python_deps</requirement> + <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement> + <requirement type="package" version="0.1.2">helperlibs</requirement> <requirement type="package" version="2.0.2">antismash</requirement> </requirements> <command>
--- a/tool_dependencies.xml Fri Oct 11 16:46:08 2013 -0400 +++ b/tool_dependencies.xml Fri Oct 11 19:24:56 2013 -0400 @@ -9,15 +9,37 @@ <package name="muscle" version="3.8.31"> <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="antismash_python_deps" version="2.0.2"> + + <package name="helperlibs" version="0.1.2"> <install version="1.0"> <actions> - <action type="setup_virtualenv">helperlibs==0.1.2 -straight.plugin==1.4.0-post-1</action> + <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> </actions> </install> <readme> - AntiSmash python dependencies (helperlibs and straight.plugin) + helperlibs python library + </readme> + </package> + <package name="straight.plugin" version="1.4.0-post-1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + straight.plugin python library </readme> </package> <package name="antismash" version="2.0.2"> @@ -37,7 +59,7 @@ do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check. --> - <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/True/g' $INSTALL_DIR/run_antismash.py</action> + <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> @@ -55,7 +77,7 @@ do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check. --> - <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/True/g' $INSTALL_DIR/run_antismash.py</action> + <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> @@ -73,7 +95,7 @@ do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check. --> - <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/True/g' $INSTALL_DIR/run_antismash.py</action> + <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> @@ -91,7 +113,7 @@ do not offer the option for genprediction and do not install glimmer and Co. For that reason deactivate the check. --> - <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/True/g' $INSTALL_DIR/run_antismash.py</action> + <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions>