Giter VIP home page Giter VIP logo

dongwei1220 / chia-pipe Goto Github PK

View Code? Open in Web Editor NEW

This project forked from thejacksonlaboratory/chia-pipe

0.0 0.0 0.0 119.79 MB

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization

License: MIT License

Shell 2.55% C++ 22.44% Python 1.38% Perl 0.49% C 61.49% R 1.78% C# 0.73% Assembly 1.85% Ada 1.16% CLIPS 0.07% CSS 0.20% Pascal 0.92% SAS 0.02% Makefile 2.22% HTML 2.15% CMake 0.11% Batchfile 0.01% DIGITAL Command Language 0.36% Module Management System 0.02% M4 0.07%

chia-pipe's Introduction

ChIA-PIPE README

The Jackson Laboratory for Genomic Medicine

Version 1.0, (November 26, 2018)

(a) Initialize outer working directory

mkdir -p testing_chia_pipe
cd testing_chia_pipe

(b) Clone ChIA-PIPE

git clone https://github.com/TheJacksonLaboratory/ChIA-PIPE.git

or (b.ii) Download ChIA-PIPE

wget [email protected]:TheJacksonLaboratory/chia_pipe.zip

(c) Install ChIA-PIPE dependencies

cd ChIA-PIPE/
dep_dir="dep_dir"
mkdir $dep_dir
bash local_install_chia_pipe_dependencies.sh -i ${dep_dir}

(d) Download test data from Dropbox

https://www.dropbox.com/sh/kiunzdfj74dpamh/AAB3u4vVGHIUSZoiPSjEYuYva?dl=0
mkdir -p fastq
cp  LDK0004-ds_*.fastq.gz  fastq

(e) Launch ChIA-PIPE

bash chia_pipe-master/0.chia_pipe_shell.sh -c chia_pipe-master/example_config_file.sh

or (e.ii) Launch ChIA-PIPE on HPC

qsub -F "--conf chia_pipe-master/example_config_file.sh" chia_pipe-master/0.chia_pipe_hpc.pbs

chia-pipe's People

Contributors

capurso-jax avatar byoungkoo avatar shengli avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.