Mercurial > repos > pjbriggs > amplicon_analysis_pipeline

comparison install_amplicon_analysis-1.3.5.sh @ 44:213b5cdecb70 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit a0f1569b4882ca4f9cee613615fe75771bbf0b23-dirty
author pjbriggs
date Mon, 09 Dec 2019 13:00:31 +0000
parents 098ad1dd7760
children 4bfa62618f7c
comparison
equal deleted inserted replaced
43:496cc0ddce3d 44:213b5cdecb70
99 echo "" 99 echo ""
100 echo -n "Rewriting conda shebangs..." 100 echo -n "Rewriting conda shebangs..."
101 rewrite_conda_shebangs 101 rewrite_conda_shebangs
102 echo "ok" 102 echo "ok"
103 echo -n "Adding conda bin to PATH..." 103 echo -n "Adding conda bin to PATH..."
104 PATH=${CONDA_BIN}:$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 }
140 - r-tidyverse=1.2.1 140 - r-tidyverse=1.2.1
141 - bioconductor-dada2=1.8 141 - bioconductor-dada2=1.8
142 - bioconductor-biomformat=1.8.0 142 - bioconductor-biomformat=1.8.0
143 EOF 143 EOF
144 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml 144 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
145 if [ $? -ne 0 ] ; then
146 fail "Non-zero exit status from 'conda env create'"
147 elif [ ! -e "${ENV_DIR}" ] ; then
148 fail "Failed to create conda environment: ${ENV_DIR} not found"
149 fi
145 echo Created conda environment in ${ENV_DIR} 150 echo Created conda environment in ${ENV_DIR}
146 cd $cwd 151 cd $cwd
147 rm -rf $wd/* 152 rm -rf $wd/*
148 rmdir $wd 153 rmdir $wd
149 # 154 #