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RAMPART + docker + gridion
#!/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'
#!/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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@sagrudd sagrudd commented Mar 30, 2020

Hei Sam - adding these thoughts to the current docker ... the container only exposes 3001 and 3000 by default - would you like any other docker ports exposed to the host?

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@SamStudio8 SamStudio8 commented Mar 30, 2020

Hey @sagrudd! Thanks for taking a look. It seems the -p $1:$1 -p $2:$2 bit in my raise_rampart.sh can open the ports as needed, so you shouldn't need to alter anything else in the container!

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@sagrudd sagrudd commented Mar 30, 2020

Cool - I'll test a little and comment further in a bit -

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@sagrudd sagrudd commented Mar 30, 2020

I have pushed ontresearch/artic_rampart:0.1.2 to 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 workflows

I will build the corresponding MinIT image and push that too - will tag both with :latest tomorrow?

Would welcome any feedback - cheers - S

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