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Open Source Science

https://github.com/amkram/panmap

🧬 🌲 Pangenome phylogenetic placement + read alignment + genotyping

https://github.com/amkram/panmap

Science Score: 26.0%

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

  • â—‹
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • â—‹
    DOI references
  • â—‹
    Academic publication links
  • â—‹
    Academic email domains
  • â—‹
    Institutional organization owner
  • â—‹
    JOSS paper metadata
  • â—‹
    Scientific vocabulary similarity
    Low similarity (2.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

🧬 🌲 Pangenome phylogenetic placement + read alignment + genotyping

Basic Info
  • Host: GitHub
  • Owner: amkram
  • Language: C++
  • Default Branch: main
  • Homepage:
  • Size: 565 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 2 years ago · Last pushed 6 months ago
Metadata Files
Readme

README.md

Installation

Docker local

git clone https://github.com/amkram/panmap

cd panmap && docker build -t panmap .

docker run -it -v .:/panmap panmap bash

The -v argument above mounts the current directory (panmap source) to /panmap in the Docker container (/panmap is the source directory within the container). This means that changes in your local panmap source dir are reflected to the container's panmap source dir. You could also separate them, e.g., -v .:/mine, which links . to /mine in the container, leaving /panmap alone.

Owner

  • Name: Alex Kramer
  • Login: amkram
  • Kind: user
  • Location: Santa Cruz, CA
  • Company: @corbett-lab

Graduate student at UC Santa Cruz - Biomolecular Engineering and Bioinformatics

GitHub Events

Total
  • Watch event: 1
  • Delete event: 1
  • Member event: 1
  • Push event: 86
  • Pull request review event: 1
  • Pull request event: 11
  • Create event: 10
Last Year
  • Watch event: 1
  • Delete event: 1
  • Member event: 1
  • Push event: 86
  • Pull request review event: 1
  • Pull request event: 11
  • Create event: 10

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 28
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Total issue authors: 0
  • Total pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 15
  • Average time to close issues: N/A
  • Average time to close pull requests: about 5 hours
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • amkram (19)
  • AlanZhangUCSC (9)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

Dockerfile docker
  • ubuntu 22.04 build
dev/Dockerfile docker
  • ubuntu 20.04 build
dev/eval/performance/Dockerfile docker
  • ubuntu 20.04 build
src/3rdparty/minimap2/setup.py pypi