Public Repository

Last pushed: 3 months ago
Short Description
A collection of Bioinformatic and statistical tools
Full Description

Tools currently available:

Basic image: ubuntu:16.04

bcftools 1.3.1 http://www.htslib.org/download/
BEDtools 2.26.0 http://bedtools.readthedocs.io/en/latest/index.html#
BWA 0.7.15 https://sourceforge.net/projects/bio-bwa/files/
Cufflinks 2.2.1 http://cole-trapnell-lab.github.io/cufflinks/install/
Diamond 0.8.38 https://github.com/bbuchfink/diamond
FastQC 0.11.5 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HiSAT2 2.0.5 https://ccb.jhu.edu/software/hisat2/index.shtml
HTSlib 1.3.1 http://www.htslib.org/download/ (includes bgzip, htsfile, tabix)
Paladin 1.4.0 https://github.com/twestbrookunh/paladin/releases
PEAR 0.9.10 https://sco.h-its.org/exelixis/web/software/pear/
Picard 2.9.2 https://github.com/broadinstitute/picard/releases
samtools 1.3.1 http://www.htslib.org/download/
seqtk 1.2 https://github.com/lh3/seqtk
SRA Toolkit 2.8.2-1 https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
STAR 2.5.2b: https://github.com/alexdobin/STAR
StringTie 1.33 https://ccb.jhu.edu/software/stringtie/
TransDecoder v3.0.1 https://github.com/TransDecoder/TransDecoder
Trimmomatic 0.36 http://www.usadellab.org/cms/?page=trimmomatic
VCFtools 0.1.14 https://github.com/vcftools/vcftools/releases

Bash tools:
c/c++ compiler (gcc)
OpenJDK 8
python
pigz (parallel version of gzip)

Under development/Need to be added still
GenomeBrowser (Struggling with X-Server access)
GATK
Beagle
MultiQC
R / RStudio

UPDATES:

VERSION 0.1.4

  • SAR Toolkit 2.8.2-1 added
  • pigz for bash added

VERSION 0.1.3

  • seqtk 1.2 added

VERSION 0.1.2

  • Picard 2.9.2 added
  • Trimmomatic 0.36 added
  • Paladin 1.4.0 added

VERSION 0.1.1

  • Diamond 0.8.4 added

VERSION 0.1

  • Initial submission
Docker Pull Command
Owner
fischuu

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