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Last pushed: 2 years ago
Short Description
NGSeasy Base Image: Power Tools
Full Description

What's in the base image??

A bunch of NGS Powertools!

  1. samtools
  2. bcftools
  3. vcftools
  4. vcflib
  5. bamUtil
  6. bedtools2
  7. ogap
  8. samblaster
  9. sambamba
  10. bamleftalign
  11. seqtk
  12. parallel

Why not separate containers per application?

A more natural / more docker-esque approach might simply be to have separate containers for each application.
This idealism belies the fact that we already need many of these tools installed on the same container
as they regularly interact in a deep way. So these should really be thought of and built as a single development environment.

Docker Pull Command
Owner
compbio

Comments (3)
arnoldliao95
a year ago

You need to use 1.0-r001 according to https://github.com/KHP-Informatics/ngseasy as of 160520
sudo docker pull compbio/ngseasy-base:1.0-r001

solomonshorseroicr
a year ago

I notice that running vcf-validator produces this error:

Can't locate Vcf.pm in @INC (you may need to install the Vcf module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.20.2 /usr/local/share/perl/5.20.2 /usr/lib/x86_64-linux-gnu/perl5/5.20 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.20 /usr/share/perl/5.20 /usr/local/lib/site_perl .) at /usr/local/bin/vcf-validator line 9.
BEGIN failed--compilation aborted at /usr/local/bin/vcf-validator line 9.

I think some components of vcftools might not be installed correctly.

solomonshorseroicr
a year ago

Hi, which image is the most current/stable release?
docker pull compbio/ngseasy-base returns:

Using default tag: latest
Pulling repository docker.io/compbio/ngseasy-base
Tag latest not found in repository docker.io/compbio/ngseasy-base