diff --git a/tools/interactive/interactivetool_bam_iobio.xml b/tools/interactive/interactivetool_bam_iobio.xml index 67b844210db..5afcd03534d 100644 --- a/tools/interactive/interactivetool_bam_iobio.xml +++ b/tools/interactive/interactivetool_bam_iobio.xml @@ -1,39 +1,27 @@ - + - qiaoy/iobio-bundle.bam-iobio:1.0-ondemand + quay.io/iobio/bam.iobio.io:0.4.0 - - 80 - + + 9001 + / /tmp/app.conf && - mv /tmp/app.conf /etc/supervisor.d/app.conf && - - /usr/bin/supervisord -c /etc/supervisord.conf + #import re + mkdir -p /bam/input_files; + #set $bam_cleaned_name = re.sub('[^\w\-\.]', '_', str($baminfile.element_identifier)) + ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' && + ln -sf '$baminfile.metadata.bam_index' '/bam/input_files/${bam_cleaned_name}.bai' && + echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bam_cleaned_name}.bai"}' >> /bam/config/config.json && + cd /bam/input_files && + node /iobio-gru-backend/src/static_server.js 9999 > /dev/null 2>&1 & + node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam > /dev/null 2>&1; ]]> - + @@ -41,6 +29,14 @@ - BAM iobio visualisation. + Required inputs: + + 1. BAM file: binary alignment map file + + The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_. + + .. _iobio project: https://iobio.io + .. _Marth lab: https://marthlab.org/ + .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/