Data

Tools

Indexes

Applications

Experiments

Open Source Science

bioinformatics

Tool including several common bioinformatics software applications

https://github.com/eipm/bioinformatics

Science Score: 75.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization eipm has institutional domain (eipm.weill.cornell.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary

Keywords

bioinformatics docker
Last synced: 10 months ago · JSON representation ·

Repository

Tool including several common bioinformatics software applications

Basic Info
  • Host: GitHub
  • Owner: eipm
  • License: mit
  • Language: Dockerfile
  • Default Branch: main
  • Homepage:
  • Size: 18.5 MB
Statistics
  • Stars: 0
  • Watchers: 9
  • Forks: 0
  • Open Issues: 1
  • Releases: 7
Topics
bioinformatics docker
Created almost 6 years ago · Last pushed 10 months ago
Metadata Files
Readme License Code of conduct Citation Security

README.md

Bioinformatics

This application provides some of the basic bioinformatics tools for development, debugging, and troubleshooting applications.

Actions Status Github EIPM Docker Hub GitHub Container Registry DOI

🤝 License

See LICENSE

📚 How to Cite

Andrea Sboner, Alexandros Sigaras, Andrea Sboner Lab, Evan Fernandez, RadiumPlatypus, & kathryn gorski. (2025). eipm/bioinformatics: v1.5.1 (v1.5.1.patched20250304). Zenodo. https://doi.org/10.5281/zenodo.14968809

Components

It includes:

  • R 4.2.2
  • bedtools (installed from distro with apt install: current version v2.30.0)
  • bcftools (installed from distro with apt install: current 1.13 (using htslib 1.13+ds)
  • vcftools (installed from distro with apt install: current 0.1.16)
  • bwa (installed from distro with apt install: current 0.7.17-r1188)
  • samtools (1.19 (using htslib 1.19))
  • pindel (latest:0.2.5b9, 20160729)
  • STAR (2.7.6a)

Note: pindel includes a fix from a non-merged branch (see Dockerfile).

Common R packages are also installed. See installPackages.R to see which ones.

Installation

To install the component for docker hub (assumining version 1.0.0):

bash docker pull eipm/bioinformatics:1.0.0

The user must have successfully logged in the docker DTR with docker login

Usage

The basic way to use this component is:

bash docker run --rm -it --name bioinfo -u $(id -u):$(id -g) eipm/bioinformatics:1.0.0 /bin/bash

If specific file mounts are needed, use the -v option (see docker run reference documentation). For example:

bash docker run --rm -it --name bioinfo -u $(id -u):$(id -g) -v /path/to/local/folder/:/path/to/internal/folder eipm/bioinformatics:1.0.0 /bin/bash

Tip: use the :ro option to mount read-only folders, e.g. -v /path/to/local/folder/:/path/to/internal/folder:ro

Combine pindel VCFs

This utility combine_pindel_vcfs.sh takes multiple pindel results and merge them [TBDs]

Owner

  • Name: Englander Institute for Precision Medicine
  • Login: eipm
  • Kind: organization
  • Location: New York, NY

Weill Cornell Medicine

Citation (CITATION.cff) 

cff-version: 1.2.0
title: eipm/bioinformatics
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - family-names: Sboner
    given-names: Andrea
    affiliation: Weill Cornell Medicine (WCM)
    orcid: 'https://orcid.org/0000-0001-6915-3070'
  - given-names: Alexandros
    family-names: Sigaras
    email: als2076@med.cornell.edu
    affiliation: Weill Cornell Medicine (WCM)
    orcid: 'https://orcid.org/0000-0002-7607-559X'
  - family-names: Gorski
    given-names: Kathryn
    affiliation: Weill Cornell Medicine (WCM)
    orcid: 'https://orcid.org/0009-0005-6277-9691'
identifiers:
  - type: doi
    value: 10.5281/zenodo.14968809
repository-code: 'https://github.com/eipm/bioinformatics'
keywords:
  - Bioinformatics
  - Precision Medicine
license: MIT

GitHub Events

Total
  • Create event: 16
  • Commit comment event: 1
  • Release event: 1
  • Delete event: 4
  • Push event: 12
  • Pull request review comment event: 1
  • Pull request review event: 9
  • Pull request event: 8
Last Year
  • Create event: 16
  • Commit comment event: 1
  • Release event: 1
  • Delete event: 4
  • Push event: 12
  • Pull request review comment event: 1
  • Pull request review event: 9
  • Pull request event: 8

Dependencies

.github/workflows/docker-publish.yml actions
  • actions/checkout v2 composite
  • docker/login-action v1 composite
Dockerfile docker
  • rocker/tidyverse 4.2.2 build
.github/workflows/monthly-patching.yml actions
  • actions/checkout v4 composite
  • actions/github-script v7 composite