Mercurial > repos > mzeidler > virana
changeset 32:47576fe39989 draft
Uploaded
| author | mzeidler |
|---|---|
| date | Mon, 23 Sep 2013 09:44:29 -0400 |
| parents | e6fb8ee52507 |
| children | 6e91b9985e80 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 4 insertions(+), 97 deletions(-) [+] |
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--- a/tool_dependencies.xml Mon Sep 23 09:30:07 2013 -0400 +++ b/tool_dependencies.xml Mon Sep 23 09:44:29 2013 -0400 @@ -4,107 +4,14 @@ <actions> <action type="setup_virtualenv"> plumbum==1.3.0 pysam==0.7.5 + numpy==1.7.1 + biopython==1.6.1 + matplotlib==1.2.1 + htseq==0.5.4 ftputil==2.2.3</action> </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="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - export PATH=$PATH:$PATH_NUMPY && - export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && - python setup.py install --install-lib $INSTALL_DIR/lib/python - </action> - <action type="set_environment"> - <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable> - </action> - </actions> - </install> - </package> - <package name="freetype" version="2.4.11"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2</action> - <action type="shell_command">./configure --prefix=$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">$INSTALL_DIR/freetype/include/</environment_variable> - </action> - </actions> - </install> - </package> - -<package name="matplotlib" version="1.2.1"> - <install version="1.0"> - <actions> - <!-- first action is always downloading --> - <action type="download_by_url">http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz</action> - - - <!-- install matplotlib --> - <action type="make_directory">$INSTALL_DIR/lib/python</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">$ENV[PYTHONPATH_NUMPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <environment_variable action="set_to" name="PYTHONPATH_MATPLOTLIB">$INSTALL_DIR/lib/python</environment_variable> - </action> - </actions> - </install> - <readme>Compiling matplotlib requires a C compiler (typically gcc) and libpng.</readme> - </package> - - <package name="htseq" version="0.5.4"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz</action> - - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - export PATH=$PATH:$PATH_NUMPY && - export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY && - python setup.py install --install-lib $INSTALL_DIR/lib/python --user --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">$ENV[PYTHONPATH_NUMPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <environment_variable action="set_to" name="PYTHONPATH_HTSEQ">$INSTALL_DIR/lib/python</environment_variable> - </action> - </actions> - </install> - </package> - <package name="samtools" version="0.1.19"> <install> <actions>