Created
March 30, 2020 12:32
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RAMPART + docker + gridion
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| #!/bin/bash | |
| USER_ID=${LOCAL_USER_ID:-9001} | |
| echo "starting with UID : $USER_ID" | |
| echo "creating RAMPART user" | |
| useradd --shell /bin/bash -u $USER_ID -o -c "" -m rampart | |
| echo "raising RAMPART on $CLIENT $SERVER" | |
| gosu rampart bash -c 'cd /data && /opt/rampart/rampart.js --verbose --clearAnnotated --protocol /opt/artic-ncov2019/rampart/ --basecalledPath /data/fastq_pass --ports $CLIENT $SERVER' |
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| #!/bin/bash | |
| sudo docker run -it -e LOCAL_USER_ID=`id -u $USER` --mount type=bind,source="$(pwd)",target=/data/ --mount type=bind,source=/PATH/TO/override_docker_workflow.sh,target=/opt/docker_workflow.sh -p $1:$1 -p $2:$2 -e CLIENT=$1 -e SERVER=$2 ontresearch/artic_rampart:0.1.1 |
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I have pushed
ontresearch/artic_rampart:0.1.2to docker hub - this includes these changes and a little subtle handling to encourage backwards compatibility with the previous command line for those users who have already scripted their workflowsI will build the corresponding MinIT image and push that too - will tag both with :latest tomorrow?
Would welcome any feedback - cheers - S