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Last pushed: 2 months ago
Short Description
Installed RNA-seq softwares in Ubuntu 16.04
Full Description

Ubuntu 16.04 for RNA-seq environment

docker pull qqep685d/rnaseq

1. Use RNA-seq software on Terminal

1-1. Starting container

docker run --rm -it -v ${PWD}:/root/data/ qqep685d/rnaseq bash

2. Use Python 3 or R on Jupyter Notebook

2-1. Starting container

docker run --rm -it -v ${PWD}:/root/data/ -p 8080:8080 qqep685d/rnaseq

2-2. Starting Notebook

Input address on Web-browser (e.g. Google Chrome, Firefox, ... etc.),
localhost:8080 (Docker for Mac), 192.168.99.100 (Docker Toolbox)
Then, input password presented on terminal.

Softwares Installed

  • miniconda3 (4.3.21)
    python (3.5), biopython (1.68), scipy, cython, numba, pandas, matplotlib, seaborn ipython-notebook
  • R (3.3.1) on Jupyter Notebook
    cummeRbund (2.16.0), edgeR (3.16.5), DESeq2 (1.14.1), limma (3.30.13), sleuth (0.28.0)
  • samtools (1.3.1)
  • bcfools (1.3.1)
  • htslib (1.3.1)
  • bedtools (2.26.0)
  • FastQC (v0.11.5)
  • PRINSEQ (0.20.4)
  • bowtie2 (2.3.2)
  • Tophat2 (2.0.14)
  • hisat2 (2.0.5)
  • cufflinks (2.2.1)
  • STAR (2.5.0a)
  • bam-readcount
  • HTSeq (0.6.1p1)
  • flexbar (v2.4)
  • kallisto (0.43.1)
  • sortmerna (2.1b)
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qqep685d

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