diff --git a/tools/interactive/interactivetool_bam_iobio.xml b/tools/interactive/interactivetool_bam_iobio.xml index 67b844210db..e6662db0660 100644 --- a/tools/interactive/interactivetool_bam_iobio.xml +++ b/tools/interactive/interactivetool_bam_iobio.xml @@ -1,46 +1,43 @@ - + - qiaoy/iobio-bundle.bam-iobio:1.0-ondemand + anderspitman/bam.iobio.io:latest - - 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)) + #set $bai_cleaned_name = re.sub('[^\w\-\.]', '_', str($baiinfile.element_identifier)) + ln -sf '$baminfile' '/bam/input_files/${bam_cleaned_name}' && + ln -sf '$baiinfile' '/bam/input_files/${bai_cleaned_name}' && + echo '{ "bam": "http://localhost:9999/${bam_cleaned_name}", "bai":"http://localhost:9999/${bai_cleaned_name}"}' >> /bam/config/config.json && + cd /bam/input_files && + node /iobio-gru-backend/src/static_server.js 9999 & + node /iobio-gru-backend/src/index.js --tools-dir=/iobio-gru-backend/tool_bin --app-dir=/bam; ]]> - + + - - - - BAM iobio visualisation. + Required inputs: + + 1. BAM file: binary alignment map file + + 2. BAI file: corresponding index 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/