Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison install_amplicon_analysis-1.3.5.sh @ 45:4bfa62618f7c draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 3dcfecb6c83d655529be44366d9e55913df9dffd
author pjbriggs
date Wed, 11 Dec 2019 13:45:05 +0000
parents 213b5cdecb70
children
comparison
equal deleted inserted replaced
44:213b5cdecb70 45:4bfa62618f7c
86 local wd=$(mktemp -d) 86 local wd=$(mktemp -d)
87 cd $wd 87 cd $wd
88 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh 88 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
89 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR} 89 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
90 echo Installed conda in ${CONDA_DIR} 90 echo Installed conda in ${CONDA_DIR}
91 echo -n "Adding conda bin to PATH..."
92 export PATH=${CONDA_BIN}:$PATH
93 echo "ok"
91 # Reset the conda version to a known working version 94 # Reset the conda version to a known working version
92 # (to avoid problems observed with e.g. conda 4.7.10) 95 # (to avoid problems observed with e.g. conda 4.7.10)
93 echo "" 96 echo ""
94 reset_conda_version 97 reset_conda_version
95 # Update the installation files 98 # Update the installation files
97 # directory path exceeds the limit for the shebang statement 100 # directory path exceeds the limit for the shebang statement
98 # in the conda files 101 # in the conda files
99 echo "" 102 echo ""
100 echo -n "Rewriting conda shebangs..." 103 echo -n "Rewriting conda shebangs..."
101 rewrite_conda_shebangs 104 rewrite_conda_shebangs
102 echo "ok"
103 echo -n "Adding conda bin to PATH..."
104 export PATH=${CONDA_BIN}:$PATH
105 echo "ok" 105 echo "ok"
106 cd $cwd 106 cd $cwd
107 rm -rf $wd/* 107 rm -rf $wd/*
108 rmdir $wd 108 rmdir $wd
109 } 109 }