Skip to content
This repository has been archived by the owner on Aug 25, 2021. It is now read-only.

Latest commit

 

History

History
87 lines (60 loc) · 2.12 KB

INSTALL.md

File metadata and controls

87 lines (60 loc) · 2.12 KB

(1) Get source code

Clone the repository and git submodules to a local folder using:

git clone http://github.com/ggirelli/gpseq-seq-gg/
cd gpseq-seq-gg
git submodule init
git submodule update

(2) Third party software

  • bwa v0.7.12-r1039
  • bowtie2 v2.2.6
  • fastqc v0.11.4
  • scan_for_matches
  • samtools v1.3.1
  • multiqc v1.5.0
  • datamash

On Ubuntu, run: sudo apt install datamash bwa bowtie2 fastqc; pip install multiqc;

scan_for_matches

Download scan_for_matches from here. Then, follow the instructions to install it. Finally, add the path of the uncompressed folder to your $PATH environment variable with:

echo -e "\nexport PATH=$PATH:path_to_scan_for_matches" >> ~/.bash_profile

fastqc

If, after installation, fastqc complains of missing files, download them from here.

(3) Required R libraries

  • argparser
  • data.table
  • ggplot2.1
  • grid
  • gridExtra
  • parallel
  • readr
  • reshape2

Install them from within R with the install.packages() command. Or run the ./INSTALL.R script.

(4) Required Python libraries

  • argparse
  • sys

Should be pre-installed with Python. Install them with pip install otherwise.

(5) Folders

Need a ~/tmp folder for sorting.

mkdir ~/tmp

(6) Submodules

Some submodules require additional steps to be used.

preseq

preseq requires you to install the GSL package (available here). Then, to install the package, move to the preseq folder and run make all:

cd lib/preseq
git submodule init
git submodule update
make all
./preseq

If everything is ready, then you should see the help page of the preseq package.

If you installed the GSL library properly (make install and make installcheck worked properly) but you get an error when compiling preseq, then you need to add the GSL library to your PATH like this:

echo -e '\nexport LD_LIBRARY_PATH="/usr/local/lib/"' >> ~/.bash_profile