Repositories list

• rfc

  Public
  Request for comments on interchangeable bioinformatics containers

  MIT License

  •9•40•38•1•Updated Jun 18, 2019Jun 18, 2019

• jgi-isolate-pipeline

  Public
  Shell

  •1•0•0•1•Updated Oct 16, 2018Oct 16, 2018

• cwl_biobox_assemblers

  Public
  Common Workflow Language

  •0•0•7•2•Updated Aug 2, 2018Aug 2, 2018

• gatb-minia

  Public
  GATB minia pipeline biobox

  bioinformaticsgenome-assembly

  Shell

  •0•0•0•0•Updated Jun 23, 2018Jun 23, 2018

• cwl_profiling_evaluation

  Public
  Shell

  •0•0•1•0•Updated May 28, 2018May 28, 2018

• cwl_biobox_profiling

  Public
  0•0•0•0•Updated May 25, 2018May 25, 2018

• ray

  Public
  Shell

  •0•0•0•0•Updated May 18, 2018May 18, 2018

• gaet

  Public
  Shell

  •1•0•0•0•Updated Dec 21, 2017Dec 21, 2017

• stride

  Public
  Shell

  •1•0•0•0•Updated Dec 15, 2017Dec 15, 2017

• jgi-single-cell-pipeline

  Public
  Biobox of assembly pipeline used at the JGI for single cell data

  Shell

  •

  Other

  •1•0•0•0•Updated Dec 9, 2017Dec 9, 2017

• fast-sga

  Public
  Shell

  •

  Other

  •0•0•0•0•Updated Dec 8, 2017Dec 8, 2017

• spades

  Public
  Shell

  •2•1•0•0•Updated Sep 13, 2017Sep 13, 2017

• unicycler

  Public
  Shell

  •0•0•0•0•Updated Sep 13, 2017Sep 13, 2017

• shovill

  Public
  Genome assembler pipeline using spades and fastq preprocessors

  Shell

  •0•0•1•0•Updated Sep 7, 2017Sep 7, 2017

• command-line-interface

  Public
  Command line interface for running and verifying biobox images

  Gherkin

  •

  MIT License

  •5•5•9•1•Updated Sep 1, 2017Sep 1, 2017

• cwl_playground

  Public
  Makefile

  •0•0•0•0•Updated Jul 14, 2017Jul 14, 2017

• bioboxes.org

  Public
  The website for bioboxes

  JavaScript

  •

  MIT License

  •8•11•0•0•Updated Jun 9, 2017Jun 9, 2017

• megahit

  Public
  Shell

  •0•0•0•0•Updated Jun 8, 2017Jun 8, 2017

• biobox-minimal-base

  Public
  A minimal base image with biobox software installed

  Shell

  •1•1•1•0•Updated Jun 8, 2017Jun 8, 2017

• bioboxes-py

  Public
  Python library for creating and running bioboxes

  1•2•3•1•Updated May 8, 2017May 8, 2017

• camiarquikr

  Public
  Shell

  •0•0•1•0•Updated Apr 25, 2017Apr 25, 2017

• quast

  Public
  Shell

  •1•0•1•0•Updated Apr 13, 2017Apr 13, 2017

• file-validator

  Public
  Validate that biobox.yaml files are correct.

  Python

  •1•0•2•0•Updated Mar 24, 2017Mar 24, 2017

• CommonKmers

  Public
  Shell

  •0•0•0•0•Updated Mar 10, 2017Mar 10, 2017

• data

  Public
  1•0•2•1•Updated Feb 17, 2017Feb 17, 2017

• light-assembler

  Public
  LightAssembler genome assembler

  Shell

  •0•2•0•0•Updated Feb 11, 2017Feb 11, 2017

• bioboxes-template

  Public
  Template for creating a biobox Docker image

  0•1•0•0•Updated Feb 11, 2017Feb 11, 2017

• focus

  Public
  Perl

  •4•0•0•0•Updated Feb 10, 2017Feb 10, 2017

• yaml2csv

  Public
  Python

  •0•1•0•0•Updated Feb 2, 2017Feb 2, 2017

• crash-test-biobox

  Public
  Docker image for testing biobox tool interfaces

  Shell

  •0•0•0•0•Updated Jan 19, 2017Jan 19, 2017