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get_results.sh
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get_results.sh
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#!/bin/bash
# $1 - project name
cd ~/Projects
cd $1
# copy the delurred biom table and the run summary
rsync -avzP -e 'ssh -o "ProxyCommand ssh [email protected] -W %h:%p"' [email protected]:work/$1/deblur/all.biom ./
rsync -avzP -e 'ssh -o "ProxyCommand ssh [email protected] -W %h:%p"' [email protected]:work/$1/process_experiment.log ./
# rsync -avzP -e 'ssh -o "ProxyCommand ssh [email protected] -W %h:%p"' [email protected]:work/$1/deblur/all.biom ./
# rsync -avzP -e 'ssh -o "ProxyCommand ssh [email protected] -W %h:%p"' [email protected]:work/$1/process_experiment.log ./
# show the region
grep region ./process_experiment.log
# if we got the biom table, delete the original fasta, trim and revcomp dir
if test -f "all.biom"; then
echo "cleaning fasta directories from server"
ssh [email protected] "ssh login8.hpc.pub.lan rm -r work/$1/fasta"
ssh [email protected] "ssh login8.hpc.pub.lan rm -r work/$1/trim"
ssh [email protected] "ssh login8.hpc.pub.lan rm -r work/$1/revcomp"
# ssh [email protected] "ssh my.hpc.pub.lan rm -r work/$1/fasta"
# ssh [email protected] "ssh my.hpc.pub.lan rm -r work/$1/trim"
# ssh [email protected] "ssh my.hpc.pub.lan rm -r work/$1/revcomp"
else
echo "all.biom not found. run failed :("
fi