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jhuapl-bio / Basestack

Basestack is a platform for rapid and real time analysis of NGS data. It provides a executable application that connects standard bionformatics tools to a user interface. It is usable on all major Linux distributions, Mac OS, and Windows 10 or later
https://basestackwebsite.readthedocs.io/en/latest/
GNU General Public License v3.0
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Multi-File Upload/Processing in Basestack? #153

Open alexandriai168 opened 1 year ago

alexandriai168 commented 1 year ago

Hello! I was wondering if it was possible to run a module on several fastq files at once. For example, I have 96 samples with a fastq for each sample. I was wondering if there's a way to run kraken2 on them on Basestack without inputting 1 file at a time.

Merritt-Brian commented 1 year ago

This feature will be made available in Basestack version 3.1. Currently we are overhauling the backend to provide increased deployment support. For example, Singularity, Docker, and Conda. The system will support a queue for scheduling jobs. However, mytax2 is available and uses kraken2. It allows you to upload a samplesheet of multiple rows that can render the sunburst for a hierarchical representation in real-time. See https://basestackwebsite.readthedocs.io/en/latest/mytax2.html