Software Installation – ALPACA on Roadrunner

List of software that needed installing to run ALPACA:

Installed all software in:


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:

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

## Add bioinformatics softwares to PATH

export PATH=${PATH}:

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/

Changed Celera Assembler directory name:

$mv /home/shared/wgs-8.3rc2 /home/shared/wgs-assembler
Step 1.
$mkdir /home/shared/test
Step 2.
$cd /home/shared/test/
Step 3.

Step three failed (which executes the 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/
Step 4. Continued with ALPACA Tests 2 & 3.

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

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