Added singularity image for create-db.
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e4245ed1dd
commit
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@ -66,3 +66,4 @@ target/
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archive
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.ropeproject
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excrawl.img
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@ -1,16 +1,11 @@
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#!/bin/bash
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module -s load apps/python/conda 2> /dev/null
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source activate mypython35
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export PATH=~/bin:$PATH
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export LD_LIBRARY_PATH=~/lib:$LD_LIBRARY_PATH
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set -o nounset
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SING_EXEC="singularity exec --pwd /opt/ExtensionCrawler -B $TMPDIR:/tmp $SING_IMG"
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printenv
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echo "The following parameter were passed: $*"
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echo "Printing the content of $ARCHIVE to force mounting:"
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ls "$ARCHIVE"
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cd "$BASEDIR"
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./ExtensionCrawler/create-db -t 1 -a "$ARCHIVE" -n $SGE_TASK_ID -N $MAX_SGE_TASK_ID $*
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$SING_EXEC ./create-db -t 1 -a "$ARCHIVE" -n $SGE_TASK_ID -N $MAX_SGE_TASK_ID $*
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@ -2,22 +2,42 @@
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set -o nounset
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set -o errexit
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BASEDIR=$( cd $(dirname "$0"); cd ..; pwd -P )
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NRJOBS=${NRJOBS:-256}
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echo "Using $NRJOBS jobs"
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JOBRANGE=${JOBRANGE:-1-$NRJOBS}
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echo "Executing jobs $JOBRANGE"
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ARCHIVE=${ARCHIVE:-$(ssh sharc.shef.ac.uk find /shared/brucker_research1/Shared/BrowserExtensions/archive/.snapshot -maxdepth 1 -name \"D*\" | sort -r | head -n1)}
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echo "Using archive: $ARCHIVE"
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TARGETDIR="${TARGETDIR:-/data/\$USER}/create-db-$(date +%Y%m%d-%H%M%S)"
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echo "Using target dir: $TARGETDIR"
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BASEDIR=$( cd $(dirname "$0"); cd ..; pwd -P )
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SING_IMG_SRC="${SING_IMG_SRC:-/shared/brucker_research1/Shared/BrowserExtensions/excrawl.img}"
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SING_IMG="$TARGETDIR/excrawl.img"
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if ! ssh sharc.shef.ac.uk [ -f "$SING_IMG_SRC" ]; then
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echo -n "$SING_IMG_SRC does not exist! Generate new image and push? (yes/abort): "
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read confirm
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if [ "$confirm" != yes ]; then
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exit 0
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fi
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echo "Creating new image ..."
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(cd "$BASEDIR/singularity"; ./build.sh)
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echo "Pushing new image ..."
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scp "$BASEDIR/singularity/excrawl.img" sharc.shef.ac.uk:"$SING_IMG_SRC"
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rm "$BASEDIR/singularity/excrawl.img"
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fi
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echo "Creating dirs ..."
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ssh sharc.shef.ac.uk mkdir -p $TARGETDIR/ExtensionCrawler
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ssh sharc.shef.ac.uk mkdir -p $TARGETDIR/logs
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echo "Pushing $BASEDIR to sharc.shef.ac.uk:$TARGETDIR/ExtensionCrawler ..."
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rsync -zr --exclude "$BASEDIR/archive" "$BASEDIR/" sharc.shef.ac.uk:"$TARGETDIR/ExtensionCrawler"
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echo "Copying $SING_IMG_SRC to $SING_IMG"
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ssh sharc.shef.ac.uk cp "$SING_IMG_SRC" "$SING_IMG"
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echo "Pushing sge script ..."
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scp "$BASEDIR/sge/create-db.sge" sharc.shef.ac.uk:"$TARGETDIR/create-db.sge"
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echo "Starting job ..."
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ssh sharc.shef.ac.uk \
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@ -28,8 +48,8 @@ ssh sharc.shef.ac.uk \
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-V \
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-m a \
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-M "msherzberg1@sheffield.ac.uk" \
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-t 1-$NRJOBS \
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-t $JOBRANGE \
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-j yes \
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-o "$TARGETDIR/logs" \
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"$TARGETDIR/ExtensionCrawler/sge/create-db.sge" \
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"$TARGETDIR/create-db.sge" \
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$*
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@ -0,0 +1,23 @@
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#!/bin/sh
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# Copyright 2017 The University of Sheffield, UK
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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if [ -f excrawl.img ]; then
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echo "Image excrawl.img exists already."
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echo "Please remove/rename the image and restart this script"
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exit 1
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else
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singularity create --size 600 excrawl.img
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sudo singularity bootstrap excrawl.img excrawl.def
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fi
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@ -0,0 +1,108 @@
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#!/bin/sh
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# Copyright 2017 The University of Sheffield, UK
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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bootstrap:debootstrap
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OSVersion: testing
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MirrorURL: https://mirror.bytemark.co.uk/debian/
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%labels
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Maintainer The LogicalHacking Team (https://logicalhacking.com)
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%setup
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%post
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###################################################################
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# Add Debian unstable as a secondary (lower priority) source
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# and update the data base of available packages.
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cat >> /etc/apt/sources.list << EOF
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deb http://ftp.us.debian.org/debian unstable main
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EOF
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cat > /etc/apt/preferences << EOF
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Package: *
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Pin: release a=testing
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Pin-Priority: 900
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Package: *
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Pin: release a=unstable
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Pin-Priority: 800
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EOF
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cat > /etc/apt/apt.conf.d/01norecommend << EOF
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APT::Install-Recommends "0";
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APT::Install-Suggests "0";
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EOF
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chmod go+r /etc/apt/preferences
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apt-get update
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###################################################################
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###################################################################
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# Install the core dependencies (Python 3.5 or later)
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# from the Debian Testing repository
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apt-get install -y python3-magic python3-crypto python3-minimal python3-pip python3-setuptools python3-mysqldb
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apt-get clean
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apt-get install -y git
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apt-get clean
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rm -rf /var/lib/apt/lists/*
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###################################################################
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###################################################################
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# Create /opt for local software (mainly cloned git repositories
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# from logicalhacking.com
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mkdir -p /opt
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chmod 755 /opt
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###################################################################
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###################################################################
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# Add the Extension Crawler repository, for more details, visit
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# https://git.logicalhacking.com/BrowserSecurity/ExtensionCrawler
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cd /opt
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git clone https://git.logicalhacking.com/BrowserSecurity/ExtensionCrawler.git
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cd ExtensionCrawler
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git checkout production
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cd ..
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pip3 install --system -e ExtensionCrawler
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ln -s /opt/ExtensionCrawler/crx-* /usr/local/bin/
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cd /
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chmod -R go+u-w /opt/ExtensionCrawler
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chmod -R go+u-w /usr/local/lib/
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chmod -R go+u-w /usr/local/bin/
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###################################################################
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###################################################################
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# Create mount/bind points for the various network drives
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# on SHARC (only useful when using the Singularity image on
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# the High-Performance Cluster of The University of Sheffield
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mkdir /scratch
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mkdir /fastdata
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mkdir /data
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mkdir /shared
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# Create nvidia driver directories to get rid of the singularity
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# warnings on sharc
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mkdir /nvbin
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mkdir /nvlib
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chmod go+u-w /scratch /fastdata /data /shared
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###################################################################
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%environment
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# We install all python modules into the container, so we do not want
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# to use any packages that the user might have installed in their home
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# directory.
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export PYTHONNOUSERSITE=1
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