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v1.5.0 #14

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v1.5.0 #14

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7c4dcae
Edit app functionality to overwrite an existing report if present. Cl…
RachelDuffin May 31, 2024
13f77f4
Set permissions of files uploaded to genomics server via rsync to all…
RachelDuffin May 31, 2024
35586a1
Update to v2 instance type. Close #13
RachelDuffin May 31, 2024
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2 changes: 1 addition & 1 deletion dxapp.json
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
"aws:us-east-1": {
"systemRequirements": {
"main": {
"instanceType": "mem1_ssd1_x2"
"instanceType": "mem1_ssd1_v2_x2"
}
}
}
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11 changes: 5 additions & 6 deletions src/code.sh
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Expand Up @@ -25,7 +25,7 @@ ssh_opts='-q -o StrictHostKeyChecking=no -o UserKnownHostsFile=/dev/null -i /hom
# Download old index.html for archiving
# Rsync options: -a archive mode for recursive copy, -v verbose outputs, -h human-readable numbers,
# -z use compression in data transfer, -e SSH command with options
rsync -avhz -e "ssh $ssh_opts" mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/index.html ${out_dir}/old_index.html
rsync --perms --chmod=Du=rw,Dgo=rw,Fu=rw,Fog=rw -avhz -e "ssh $ssh_opts" mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/index.html ${out_dir}/old_index.html

# Create a variable containing the SSH command arguments required to determine if the file exists.
# These arguments include the options to connect to the server and the bash 'test' command, with the
Expand All @@ -34,17 +34,16 @@ file_exists_test="$ssh_opts mokaguys@genomics.viapath.co.uk test -e /var/www/htm

# Test if the file exists on the Viapath Genomics server using ssh and ${file_exist_test} arguments. Exit with error code 1 if True.
if ssh ${file_exists_test}; then
echo "ERROR: ${multiqc_html_name} exists at /var/www/html/mokaguys/multiqc/reports/." 1>&2
exit 1
echo "${multiqc_html_name} exists at /var/www/html/mokaguys/multiqc/reports/. Overwriting" 1>&2
fi

# Upload the multiqc html to the multiqc reports directory
rsync -avhz -e "ssh $ssh_opts" ${multiqc_html_path} mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/reports/${multiqc_html_name}
rsync --perms --chmod=Du=rw,Dgo=rw,Fu=rw,Fog=rw -avhz -e "ssh $ssh_opts" ${multiqc_html_path} mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/reports/${multiqc_html_name}
#Run docker image to create new_index.html
docker run -v `pwd`:/home/dnanexus seglh/upload_index:latest ${out_dir}/old_index.html ${multiqc_html_path} ${out_dir}/new_index.html

# Upload new index.html to server
rsync -avhz -e "ssh $ssh_opts" ${out_dir}/new_index.html mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/index.html
rsync --perms --chmod=Du=rw,Dgo=rw,Fu=rw,Fog=rw -avhz -e "ssh $ssh_opts" ${out_dir}/new_index.html mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/index.html

if [[ "$upload_data_files" == "true" ]]; then
# capture the project name from the multiqc html name (project_name-multiqc.html)
Expand All @@ -64,7 +63,7 @@ if [[ "$upload_data_files" == "true" ]]; then
# for each data file in $multiqc_data_input upload to server
for data_file_path in "${multiqc_data_input_path[@]}"; do
# Upload the multiqc data files to the multiqc reports directory
rsync -avhz -e "ssh $ssh_opts" ${data_file_path} mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/trend_analysis/multiqc_data/${project_name}
rsync --perms --chmod=Du=rw,Dgo=rw,Fu=rw,Fog=rw -avhz -e "ssh $ssh_opts" ${data_file_path} mokaguys@genomics.viapath.co.uk:/var/www/html/mokaguys/multiqc/trend_analysis/multiqc_data/${project_name}
done
fi

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