Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

changeset 3:b9e2b3dd392d draft

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Removed unwanted changes to install_tool_deps.sh in previous upload.
author pjbriggs
date Wed, 25 Apr 2018 03:50:53 -0400
parents a898ee628343
children 013bf1e2cc8f
files install_tool_deps.sh
diffstat 1 files changed, 7 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- a/install_tool_deps.sh	Wed Apr 25 03:45:37 2018 -0400
+++ b/install_tool_deps.sh	Wed Apr 25 03:50:53 2018 -0400
@@ -338,9 +338,6 @@
     export ATLAS_ROOT_PATH=$INSTALL_DIR
     export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
     export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
-    # Make installation directories
-    mkdir -p $INSTALL_DIR/bin
-    mkdir -p $INSTALL_DIR/lib/python2.7/site-packages
     # Numpy 1.7.1
     local wd=$(mktemp -d)
     echo Moving to $wd
@@ -363,49 +360,13 @@
     popd
     rm -rf $wd/*
     rmdir $wd
-    # Setuptools 36.4.0
-    install_python_package $INSTALL_DIR setuptools 38.2.4 \
-	https://github.com/pypa/setuptools/archive/v38.2.4.tar.gz \
-	setuptools-38.2.4
-    # Distribute 0.6.28
-    ##local wd=$(mktemp -d)
-    ##echo Moving to $wd
-    ##pushd $wd
-    ##wget -q https://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz
-    ##tar -zxvf distribute-0.6.28.tar.gz
-    ##cd distribute-0.6.28
-    ##sed -i 's,index_url="http://pypi.python.org/simple",index_url="https://pypi.python.org/simple",g' setuptools/package_index.py
-    ##sed -i 's,"http://pypi.python.org/simple","https://pypi.python.org/simple",g' setuptools/command/easy_install.py
-    ##/bin/bash <<EOF
-##export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
-##export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
-##python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
-##EOF
-    ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
-    ##popd
-    ##rm -rf $wd/*
-    ##rmdir $wd
-    # Matplotlib 1.3.1
-    local wd=$(mktemp -d)
-    echo Moving to $wd
-    pushd $wd
-    wget -q https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz
-    tar -zxvf matplotlib-1.3.1.tar.gz
-    cd matplotlib-1.3.1
-    sed -i 's,http://pypi.python.org/packages/source/d/distribute/,https://pypi.python.org/packages/source/d/distribute/,g' distribute_setup.py
-    /bin/bash <<EOF
-export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
-export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
-python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
-EOF
-    ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
-    popd
-    rm -rf $wd/*
-    rmdir $wd
-    # Remaining Python packages
-    ##install_python_package $INSTALL_DIR matplotlib 1.3.1 \
-	##https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
-	##matplotlib-1.3.1
+    # Python packages
+    ##install_python_package $INSTALL_DIR numpy 1.7.1 \
+    ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
+    ## numpy-1.7.1
+    install_python_package $INSTALL_DIR matplotlib 1.3.1 \
+	https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
+	matplotlib-1.3.1
     install_python_package $INSTALL_DIR qiime 1.8.0 \
 	https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
 	qiime-1.8.0