Warning: Horrible markdown formatting below! Will update if I can figure out an easy fix.

List of software that needed installing to run ALPACA:

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:

$sudo chown -R :sudo /home/shared

Compiled Celera Assembler from source (per the ALPACA requirements). This is the source file that I used: http://ift.tt/2xJvsID

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

## 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

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

$source ~/.bashrc

Followed the ALPACA test instructions 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:

$mv /home/shared/wgs-8.3rc2 /home/shared/wgs-assembler
  1. $mkdir /home/shared/test
$cd /home/shared/test/
  1. $../alpaca/scripts/run_example.sh

    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:

    $sudo chmod +x /home/shared/alpaca/scripts/run_example.sh
  2. Continued with ALPACA Tests 2 & 3.

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

from Sam’s Notebook http://ift.tt/2xJuyeV

Software Installation – ALPACA on Roadrunner
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