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pull t-rex #26

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merged 1 commit into from
Feb 20, 2024
Merged

pull t-rex #26

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2 changes: 1 addition & 1 deletion autoscale.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@


JS2AUTOSCALING="/home/ubuntu/t-rex-monitor/js2-autoscaling.sh"
CONFIG="/home/ubuntu/crux/crux/vars/crux_vars.sh"
CONFIG="/home/ubuntu/t-rex/crux/vars/crux_vars.sh"
SETUP_CONFIG="/home/ubuntu/t-rex-monitor/vm_vars.sh"
QUEUES=("/etc/ben/queue/qc.ini" "/etc/ben/queue/assign.ini" "/etc/ben/queue/assignxl.ini" "/etc/ben/queue/ecopcr.ini" "/etc/ben/queue/blast.ini" "/etc/ben/queue/ac.ini" "/etc/ben/queue/newick.ini" "/etc/ben/queue/tronko.ini")

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16 changes: 8 additions & 8 deletions main/crux-pssh.sh
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Expand Up @@ -29,15 +29,15 @@ if [ "$(wc -l < tmphost)" -eq 1 ]; then
host=$(cat tmphost)

if [ "$BRANCH" = "master" ]; then
ssh "$host" "git clone https://github.com/CALeDNA/crux.git"
ssh "$host" "git clone https://github.com/eDNA-Explorer/t-rex.git"
else
ssh "$host" "git clone -b $BRANCH https://github.com/CALeDNA/crux.git"
ssh "$host" "git clone -b $BRANCH https://github.com/eDNA-Explorer/t-rex.git"
fi

scp "$CONFIG" "$host:/home/$USER/crux/crux/vars/"
scp "$CONFIG" "$host:/home/$USER/t-rex/crux/vars/"

if [ "$ASSIGN" = "TRUE" ]; then
scp ./.env $host:/home/$USER/crux/tronko/assign/jwt/.env
scp ./.env $host:/home/$USER/t-rex/tronko/assign/jwt/.env
fi

ssh "$host" "sudo apt install awscli -y"
Expand All @@ -49,16 +49,16 @@ if [ "$(wc -l < tmphost)" -eq 1 ]; then
fi
else
if [ "$ASSIGN" = "TRUE" ]; then
parallel-scp -h tmphost ./.env /home/$USER/crux/tronko/assign/jwt/.env
parallel-scp -h tmphost ./.env /home/$USER/t-rex/tronko/assign/jwt/.env
fi

if [ "$BRANCH" = "master" ]; then
parallel-ssh -i -t 0 -h tmphost "git clone https://github.com/CALeDNA/crux.git"
parallel-ssh -i -t 0 -h tmphost "git clone https://github.com/eDNA-Explorer/t-rex.git"
else
parallel-ssh -i -t 0 -h tmphost "git clone -b $BRANCH https://github.com/CALeDNA/crux.git"
parallel-ssh -i -t 0 -h tmphost "git clone -b $BRANCH https://github.com/eDNA-Explorer/t-rex.git"
fi

parallel-scp -h tmphost $CONFIG /home/$USER/crux/crux/vars/
parallel-scp -h tmphost $CONFIG /home/$USER/t-rex/crux/vars/

parallel-ssh -i -t 0 -h tmphost "sudo apt install awscli -y"

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2 changes: 1 addition & 1 deletion vm_setup.sh
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Expand Up @@ -14,7 +14,7 @@ PRIMERS=""
START=0
NODES=0
BENSERVER=""
VARS="/home/ubuntu/crux/crux/vars/crux_vars.sh"
VARS="/home/ubuntu/t-rex/crux/vars/crux_vars.sh"
DASHBOARD=/var/lib/grafana/dashboards/overview.json
while getopts "u:f:i:k:j:n:m:b:s:w:v:c:p:o:e:" opt; do
case $opt in
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