---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2017-10-31 19:45:49+00:00
layout: post
slug: software-installation-alpaca-on-roadrunner
title: Software Installation - ALPACA on Roadrunner
categories:
  - 2017
  - Miscellaneous
tags:
  - ALPACA
  - Celera
  - roadrunner
---

List of software that needed installing to run ALPACA:





  * [ALPACA](https://github.com/VicugnaPacos/ALPACA)



  * [Celera Assembler](https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/)



  * [samtools](https://www.htslib.org/download/)



  * [bowtie2](https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3.1/)



  * [ECtools](https://github.com/jgurtowski/ectools/releases)






Installed all software in:

`/home/shared/`

Had to change permissions on `/home/shared/`. Used the following to change permissions recursively (-R) to allow all admin (i.e. sudo group) users to read/write in this directory:


    
    <code>$sudo chown -R :sudo /home/shared</code>



Compiled Celera Assembler from source ([per the ALPACA requirements](https://github.com/VicugnaPacos/ALPACA#install-celera-assembler)). This is the source file that I used: [https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc2.tar.bz2/download](https://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc2.tar.bz2)

Added all software to my system PATH by adding the following to my `~./bashrc` file:

[code lang=text]
## Add bioinformatics softwares to PATH

export PATH=${PATH}:
/home/shared/alpaca:
/home/shared/Bismark:
/home/shared/bowtie2-2.3.3.1-linux-x86_64:
/home/shared/ectools-0.1:
/home/shared/PBSuite_15.8.24/bin:
/home/shared/pecan/bin:
/home/shared/samtools-1.6/bin:
/home/shared/wgs-assembler/Linux-amd64/bin
[/code]

After adding that info to the bottom of my `~./bashrc` file, I re-loaded the file into system memory by sourcing the file:


    
    <code>$source ~/.bashrc</code>



Followed the [ALPACA test instructions](https://github.com/VicugnaPacos/ALPACA#test) to confirm proper installation. More specific test instructions are actually located at the top of this file: `/home/shared/alpaca/scripts/run_example.sh`

Changed Celera Assembler directory name:


    
    <code>$mv /home/shared/wgs-8.3rc2 /home/shared/wgs-assembler</code>





##### Step 1.




    
    <code>$mkdir /home/shared/test</code>





##### Step 2.




    
    <code>$cd /home/shared/test/</code>





##### Step 3.




    
    <code>$../alpaca/scripts/run_example.sh</code>



Step three failed (which executes the `run_example.sh` script) due to permission problems.

Realized the script file didn't have execute perimssions so I added execute permissions with the following command:


    
    <code>$sudo chmod +x /home/shared/alpaca/scripts/run_example.sh</code>





##### Step 4. Continued with [ALPACA Tests 2 & 3.](https://github.com/VicugnaPacos/ALPACA#test)



Everything tested successfully. Will try to get an assembly running with our PacBio and Illumina data.