# HG changeset patch
# User mzeidler
# Date 1379947807 14400
# Node ID 55374722c6f5f3d403b9e9bbb054a0375a523901
# Parent e59d8289935d47ced05794978e2120409e5ab427
Uploaded
diff -r e59d8289935d -r 55374722c6f5 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Sep 23 10:32:01 2013 -0400
+++ b/tool_dependencies.xml Mon Sep 23 10:50:07 2013 -0400
@@ -4,14 +4,107 @@
plumbum==1.3.0
pysam==0.7.5
- numpy==1.5.1
- matplotlib==1.2.1
- biopython==1.61
- htseq==0.5.4
ftputil==2.2.3
+
+
+
+ https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz
+ $INSTALL_DIR/lib/python
+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
+
+ $INSTALL_DIR/lib/python
+ $INSTALL_DIR/lib/python
+ $INSTALL_DIR/bin
+
+
+
+
+
+
+
+
+ http://downloads.sourceforge.net/project/freetype/freetype2/2.4.11/freetype-2.4.11.tar.bz2
+ ./configure --prefix=$INSTALL_DIR/freetype/
+ make
+ make install
+
+ $INSTALL_DIR/freetype/bin/
+ $INSTALL_DIR/freetype/lib/
+ $INSTALL_DIR/freetype/include/
+
+
+
+
+
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+
+
+
+ http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.1/matplotlib-1.2.1.tar.gz
+
+
+
+ $INSTALL_DIR/lib/python
+ echo "### PYTHONPATH = $PYTHONPATH, PYTHONPATH_NUMPY = $PYTHONPATH_NUMPY"
+ export PYTHONPATH=$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
+
+ $INSTALL_DIR/lib/python
+ $ENV[PYTHONPATH_NUMPY]
+ $ENV[PATH_NUMPY]
+ $INSTALL_DIR/lib/python
+
+
+
+ Compiling matplotlib requires a C compiler (typically gcc) and libpng.
+
+
+
+
+ https://pypi.python.org/packages/source/b/biopython/biopython-1.61.tar.gz
+ $INSTALL_DIR/lib/python
+
+ export PYTHONPATH=$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
+
+
+ $INSTALL_DIR/lib/python
+ $ENV[PYTHONPATH_NUMPY]
+ $ENV[PATH_NUMPY]
+ $INSTALL_DIR/lib/python
+
+
+
+
+
+
+
+ https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p3.tar.gz
+
+ $INSTALL_DIR/lib/python
+
+ export PYTHONPATH=$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
+
+
+ $INSTALL_DIR/lib/python
+ $ENV[PYTHONPATH_NUMPY]
+ $ENV[PATH_NUMPY]
+ $INSTALL_DIR/lib/python
+
+
+
+
+