Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison install_tool_deps.sh @ 2:a898ee628343 draft

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Updated to version 1.2.1.0
author pjbriggs
date Wed, 25 Apr 2018 03:45:37 -0400
parents b433086738d6
children b9e2b3dd392d
comparison
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1:a00f366adc45 2:a898ee628343
32 python setup.py install --prefix=$install_dir --install-scripts=$install_dir/bin --install-lib=$install_dir/lib/python2.7/site-packages >>$INSTALL_DIR/INSTALLATION.log 2>&1 32 python setup.py install --prefix=$install_dir --install-scripts=$install_dir/bin --install-lib=$install_dir/lib/python2.7/site-packages >>$INSTALL_DIR/INSTALLATION.log 2>&1
33 EOF 33 EOF
34 popd 34 popd
35 rm -rf $wd/* 35 rm -rf $wd/*
36 rmdir $wd 36 rmdir $wd
37 }
38 function install_amplicon_analysis_pipeline_1_2_1() {
39 install_amplicon_analysis_pipeline $1 1.2.1
37 } 40 }
38 function install_amplicon_analysis_pipeline_1_1() { 41 function install_amplicon_analysis_pipeline_1_1() {
39 install_amplicon_analysis_pipeline $1 1.1 42 install_amplicon_analysis_pipeline $1 1.1
40 } 43 }
41 function install_amplicon_analysis_pipeline_1_0() { 44 function install_amplicon_analysis_pipeline_1_0() {
333 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas 336 export ATLAS_BLAS_LIB_DIR=$INSTALL_DIR/lib/atlas
334 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas 337 export ATLAS_LAPACK_LIB_DIR=$INSTALL_DIR/lib/atlas
335 export ATLAS_ROOT_PATH=$INSTALL_DIR 338 export ATLAS_ROOT_PATH=$INSTALL_DIR
336 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH 339 export LD_LIBRARY_PATH=$INSTALL_DIR/lib:$LD_LIBRARY_PATH
337 export LD_LIBRARY_PATH=$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 $INSTALL_DIR/lib/python2.7/site-packages
338 # Numpy 1.7.1 344 # Numpy 1.7.1
339 local wd=$(mktemp -d) 345 local wd=$(mktemp -d)
340 echo Moving to $wd 346 echo Moving to $wd
341 pushd $wd 347 pushd $wd
342 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz 348 wget -q https://depot.galaxyproject.org/software/numpy/numpy_1.7_src_all.tar.gz
355 export ATLAS=$ATLAS_ROOT_PATH 361 export ATLAS=$ATLAS_ROOT_PATH
356 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin 362 python setup.py install --install-lib $INSTALL_DIR/lib/python2.7 --install-scripts $INSTALL_DIR/bin
357 popd 363 popd
358 rm -rf $wd/* 364 rm -rf $wd/*
359 rmdir $wd 365 rmdir $wd
360 # Python packages 366 # Setuptools 36.4.0
361 ##install_python_package $INSTALL_DIR numpy 1.7.1 \ 367 install_python_package $INSTALL_DIR setuptools 38.2.4 \
362 ## https://pypi.python.org/packages/84/fb/5e9dfeeb5d8909d659e6892c97c9aa66d3798fad50e1d3d66b3c614a9c35/numpy-1.7.1.tar.gz \ 368 https://github.com/pypa/setuptools/archive/v38.2.4.tar.gz \
363 ## numpy-1.7.1 369 setuptools-38.2.4
364 install_python_package $INSTALL_DIR matplotlib 1.3.1 \ 370 # Distribute 0.6.28
365 https://pypi.python.org/packages/d4/d0/17f17792a4d50994397052220dbe3ac9850ecbde0297b7572933fa4a5c98/matplotlib-1.3.1.tar.gz \ 371 ##local wd=$(mktemp -d)
366 matplotlib-1.3.1 372 ##echo Moving to $wd
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
367 install_python_package $INSTALL_DIR qiime 1.8.0 \ 409 install_python_package $INSTALL_DIR qiime 1.8.0 \
368 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \ 410 https://github.com/biocore/qiime/archive/1.8.0.tar.gz \
369 qiime-1.8.0 411 qiime-1.8.0
370 install_python_package $INSTALL_DIR pycogent 1.5.3 \ 412 install_python_package $INSTALL_DIR pycogent 1.5.3 \
371 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \ 413 https://pypi.python.org/packages/1f/9f/c6f6afe09a3d62a6e809c7745413ffff0f1e8e04d88ab7b56faedf31fe28/cogent-1.5.3.tgz \
684 fi 726 fi
685 if [ ! -d "$TOP_DIR" ] ; then 727 if [ ! -d "$TOP_DIR" ] ; then
686 mkdir -p $TOP_DIR 728 mkdir -p $TOP_DIR
687 fi 729 fi
688 # Install dependencies 730 # Install dependencies
689 install_amplicon_analysis_pipeline_1_1 $TOP_DIR 731 install_amplicon_analysis_pipeline_1_2_1 $TOP_DIR
690 install_cutadapt_1_11 $TOP_DIR 732 install_cutadapt_1_11 $TOP_DIR
691 install_sickle_1_33 $TOP_DIR 733 install_sickle_1_33 $TOP_DIR
692 install_bioawk_27_08_2013 $TOP_DIR 734 install_bioawk_27_08_2013 $TOP_DIR
693 install_pandaseq_2_8_1 $TOP_DIR 735 install_pandaseq_2_8_1 $TOP_DIR
694 install_spades_3_5_0 $TOP_DIR 736 install_spades_3_5_0 $TOP_DIR