1_preinstall_nanshe_workflow.sh

#!/bin/bash


# Copyright (c) 2016-2019, John Kirkham, Howard Hughes Medical Institute
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#    this list of conditions and the following disclaimer.
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# 2. Redistributions in binary form must reproduce the above copyright notice,
#    this list of conditions and the following disclaimer in the documentation
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# 3. Neither the name of the copyright holder nor the names of its contributors
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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# Fix up the bash profile.
touch ~/.bash_profile
if ! $(grep -q "source ~/.nanshe_workflow.sh" ~/.bash_profile);
then
  echo "" >> ~/.bash_profile
  echo "source ~/.nanshe_workflow.sh" >> ~/.bash_profile
fi

# (Re)Create our bash startup script to setup the environment.
rm -f ~/.nanshe_workflow.sh
touch ~/.nanshe_workflow.sh
cat > ~/.nanshe_workflow.sh << 'EOF'
# Set the temporary directory.
TMPDIR="$HOME/tmp"
TEMP="$TMPDIR"
TMP="$TMPDIR"
export TMPDIR TEMP TMP
mkdir -p "$TMPDIR"

# Export Grid Engine and DRMAA variables, if available.
# May not be available when using Linux locally or Windows with Git Bash.
if [[ -f /sge/current/default/common/settings.sh ]]; then
    source /sge/current/default/common/settings.sh
    export SGE_DRMAA_LIBRARY_PATH="$SGE_ROOT/lib/lx-amd64/libdrmaa.so.1.0"
    export DRMAA_LIBRARY_PATH="$SGE_DRMAA_LIBRARY_PATH"
fi
# Export LSF variables, if available.
# May not be available when using Linux locally or Windows with Git Bash.
if [[ -f /misc/lsf/conf/profile.lsf ]]; then
    source /misc/lsf/conf/profile.lsf
    export LSB_STDOUT_DIRECT="Y"
    export LSB_JOB_REPORT_MAIL="N"
    export LSF_DRMAA_LIBRARY_PATH="/misc/sc/lsf-glibc2.3/lib/libdrmaa.so.0.1.1"
    export DRMAA_LIBRARY_PATH="$LSF_DRMAA_LIBRARY_PATH"
fi

# Set the Jupyter runtime directory in the user's home.
# This simply follows the recommendation of our cluster admins
# to redirect this to a different location than XDG_RUNTIME_DIR.
# This is just what Jupyter picks when XDG_RUNTIME_DIR is disabled.
export JUPYTER_RUNTIME_DIR="$HOME/.local/share/jupyter/runtime"
EOF