Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison install_tool_deps.sh @ 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
comparison
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2:a898ee628343 3:b9e2b3dd392d
336 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas 336 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas
337 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas 337 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas
338 export ATLAS_ROOT_PATH=$INSTALL_DIR 338 export ATLAS_ROOT_PATH=$INSTALL_DIR
339 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH 339 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
340 export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH 340 export LD_LIBRARY_PATH=$INSTALL_DIR/lib/atlas:$LD_LIBRARY_PATH
341 # Make installation directories
342 mkdir -p $INSTALL_DIR/bin
343 mkdir -p $INSTALL_DIR/lib/python2.7/site-packages
344 # Numpy 1.7.1 341 # Numpy 1.7.1
345 local wd=$(mktemp -d) 342 local wd=$(mktemp -d)
346 echo Moving to $wd 343 echo Moving to $wd
347 pushd $wd 344 pushd $wd
348 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz 345 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz
361 export ATLAS=$ATLAS_ROOT_PATH 358 export ATLAS=$ATLAS_ROOT_PATH
362 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin 359 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
363 popd 360 popd
364 rm -rf $wd/* 361 rm -rf $wd/*
365 rmdir $wd 362 rmdir $wd
366 # Setuptools 36.4.0 363 # Python packages
367 install_python_package $INSTALL_DIR setuptools 38.2.4 \ 364 ##install_python_package $INSTALL_DIR numpy 1.7.1 \
368 https://github.com/pypa/setuptools/archive/v38.2.4.tar.gz \ 365 ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \
369 setuptools-38.2.4 366 ## numpy-1.7.1
370 # Distribute 0.6.28 367 install_python_package $INSTALL_DIR matplotlib 1.3.1 \
371 ##local wd=$(mktemp -d) 368 https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
372 ##echo Moving to $wd 369 matplotlib-1.3.1
373 ##pushd $wd
374 ##wget -q https://pypi.python.org/packages/source/d/distribute/distribute-0.6.28.tar.gz
375 ##tar -zxvf distribute-0.6.28.tar.gz
376 ##cd distribute-0.6.28
377 ##sed -i 's,index_url="http://pypi.python.org/simple",index_url="https://pypi.python.org/simple",g' setuptools/package_index.py
378 ##sed -i 's,"http://pypi.python.org/simple","https://pypi.python.org/simple",g' setuptools/command/easy_install.py
379 ##/bin/bash <<EOF
380 ##export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
381 ##export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
382 ##python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
383 ##EOF
384 ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
385 ##popd
386 ##rm -rf $wd/*
387 ##rmdir $wd
388 # Matplotlib 1.3.1
389 local wd=$(mktemp -d)
390 echo Moving to $wd
391 pushd $wd
392 wget -q https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz
393 tar -zxvf matplotlib-1.3.1.tar.gz
394 cd matplotlib-1.3.1
395 sed -i 's,http://pypi.python.org/packages/source/d/distribute/,https://pypi.python.org/packages/source/d/distribute/,g' distribute_setup.py
396 /bin/bash <<EOF
397 export PYTHONPATH=$INSTALL_DIR:$PYTHONPATH && \
398 export PYTHONPATH=$INSTALL_DIR/lib/python2.7/site-packages:$PYTHONPATH && \
399 python setup.py install --prefix=$INSTALL_DIR --install-scripts=$INSTALL_DIR/bin --install-lib=$INSTALL_DIR/lib/python2.7/site-packages
400 EOF
401 ##python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
402 popd
403 rm -rf $wd/*
404 rmdir $wd
405 # Remaining Python packages
406 ##install_python_package $INSTALL_DIR matplotlib 1.3.1 \
407 ##https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \
408 ##matplotlib-1.3.1
409 install_python_package $INSTALL_DIR qiime 1.8.0 \ 370 install_python_package $INSTALL_DIR qiime 1.8.0 \
410 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \ 371 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
411 qiime-1.8.0 372 qiime-1.8.0
412 install_python_package $INSTALL_DIR pycogent 1.5.3 \ 373 install_python_package $INSTALL_DIR pycogent 1.5.3 \
413 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \ 374 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \