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Open Source Science

https://github.com/arcadia-science/2022-tx-not-in-gx

https://github.com/arcadia-science/2022-tx-not-in-gx

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: Arcadia-Science
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 612 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 9
  • Releases: 0
Created over 3 years ago · Last pushed over 3 years ago

https://github.com/Arcadia-Science/2022-tx-not-in-gx/blob/main/ 


## Getting started with this repository

This repository uses snakemake to run the pipeline and conda to manage software environments and installations.
You can find operating system-specific instructions for installing miniconda [here](https://docs.conda.io/en/latest/miniconda.html).
After installing conda and [mamba](https://mamba.readthedocs.io/en/latest/), run the following command to create the pipeline run environment.
We installaed Miniconda3 version `py39_4.12.0` and mamba version `0.15.3`.

```
mamba env create -n tx_gx --file environment.yml
conda activate tx_gx
```

To start the pipeline, run:
```
snakemake --use-conda -j 2
```

### Running this repository on AWS

This repository was executed on an AWS EC2 instance (Ubuntu 22.04 LTS ami-085284d24fe829cd0, t2.2xlarge, 200 GiB EBS `gp2` root storage).
The instance was configured using the following commands:

```
curl -JLO https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh # download the miniconda installation script
bash Miniconda3-latest-Linux-x86_64.sh # run the miniconda installation script. Accept the license and follow the defaults.
source ~/.bashrc # source the .bashrc for miniconda to be available in the environment

# configure miniconda channel order
conda config --add channels defaults 
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda install mamba # install mamba for faster software installation.
```

## Papers that inspired this project

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1873-2
https://www.biorxiv.org/content/10.1101/2022.09.25.509396v1

Owner

  • Name: Arcadia Science
  • Login: Arcadia-Science
  • Kind: organization
  • Location: United States of America

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Dependencies

environment.yml conda
  • pandas 1.4.3.*
  • snakemake-minimal 7.12.1.*