Mercurial > repos > mzeidler > virana
changeset 31:e6fb8ee52507 draft
Uploaded
| author | mzeidler |
|---|---|
| date | Mon, 23 Sep 2013 09:30:07 -0400 |
| parents | 3cee6b37cdcf |
| children | 47576fe39989 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 39 insertions(+), 31 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Sep 23 09:19:22 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 23 09:30:07 2013 -0400 @@ -1,10 +1,4 @@ <tool_dependency> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="freetype" version="2.4.11"> - <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package> <package name="virana_python" version="1.0"> <install version="1.0"> <actions> @@ -14,15 +8,24 @@ </actions> </install> </package> + <package name="numpy" version="1.7.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.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 --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action> + <action type="set_environment"> + <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable name="PYTHONPATH_NUMPY" action="set_to">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + </package> <package name="biopython" version="1.61"> <install version="1.0"> <actions> <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && @@ -39,29 +42,36 @@ </actions> </install> </package> + <package name="freetype" version="2.4.11"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action> + <action type="shell_command">./configure --prefix=$INSTALL_DIR/freetype/</action> + <action type="shell_command">make</action> + <action type="shell_command">make install</action> + <action type="set_environment"> + <environment_variable name="PATH" action="append_to">$INSTALL_DIR/freetype/bin/</environment_variable> + <environment_variable name="FREETYPE_LIB_DIR" action="set_to">$INSTALL_DIR/freetype/lib/</environment_variable> + <environment_variable name="FREETYPE_INCLUDE_DIR" action="set_to">$INSTALL_DIR/freetype/include/</environment_variable> + </action> + </actions> + </install> + </package> + <package name="matplotlib" version="1.2.1"> <install version="1.0"> <actions> <!-- first action is always downloading --> <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - <repository changeset_revision="fe5cfaf931ff" name="package_freetype_2_4" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="freetype" version="2.4.11" /> - </repository> - </action> <!-- install matplotlib --> <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY && - export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/ && - export LIBRARY_PATH=$FREETYPE_LIB_DIR && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin - </action> + <action type="shell_command">echo "### PYTHONPATH = $PYTHONPATH, PYTHONPATH_NUMPY = $PYTHONPATH_NUMPY"</action> + <action type="shell_command">export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH && + export CPLUS_INCLUDE_PATH=$FREETYPE_INCLUDE_DIR:$FREETYPE_INCLUDE_DIR/freetype2/:$CPLUS_INCLUDE_PATH && + export LIBRARY_PATH=$FREETYPE_LIB_DIR:$LIBRARY_PATH && + python setup.py install --home $INSTALL_DIR --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="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> @@ -70,16 +80,14 @@ </action> </actions> </install> + <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme> </package> + <package name="htseq" version="0.5.4"> <install version="1.0"> <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="b7ff4a8c58df" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - </action> + <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&