Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison install_tool_deps.sh @ 4:013bf1e2cc8f draft

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Updated to Amplicon_Analysis_pipeline v1.2.2.
author pjbriggs
date Wed, 13 Jun 2018 07:43:57 -0400
parents b9e2b3dd392d
children
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3:b9e2b3dd392d 4:013bf1e2cc8f
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_2() {
39 install_amplicon_analysis_pipeline $1 1.2.2
37 } 40 }
38 function install_amplicon_analysis_pipeline_1_2_1() { 41 function install_amplicon_analysis_pipeline_1_2_1() {
39 install_amplicon_analysis_pipeline $1 1.2.1 42 install_amplicon_analysis_pipeline $1 1.2.1
40 } 43 }
41 function install_amplicon_analysis_pipeline_1_1() { 44 function install_amplicon_analysis_pipeline_1_1() {
687 fi 690 fi
688 if [ ! -d "$TOP_DIR" ] ; then 691 if [ ! -d "$TOP_DIR" ] ; then
689 mkdir -p $TOP_DIR 692 mkdir -p $TOP_DIR
690 fi 693 fi
691 # Install dependencies 694 # Install dependencies
692 install_amplicon_analysis_pipeline_1_2_1 $TOP_DIR 695 install_amplicon_analysis_pipeline_1_2_2 $TOP_DIR
693 install_cutadapt_1_11 $TOP_DIR 696 install_cutadapt_1_11 $TOP_DIR
694 install_sickle_1_33 $TOP_DIR 697 install_sickle_1_33 $TOP_DIR
695 install_bioawk_27_08_2013 $TOP_DIR 698 install_bioawk_27_08_2013 $TOP_DIR
696 install_pandaseq_2_8_1 $TOP_DIR 699 install_pandaseq_2_8_1 $TOP_DIR
697 install_spades_3_5_0 $TOP_DIR 700 install_spades_3_5_0 $TOP_DIR