Revision as of 14:40, 24 April 2015

Installing PBcR on Abel

The PBcR package is not available as an installed Abel module. However, installation does not require more than downloading and extracting the program. Additionally, a utility Java script may be downloaded that will convert fasta read data into the required fastq format. PBcR can be downloaded from the "Whole-Genome Shotgun Assembler" sourceforge web page:

http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/

Clicking on the current version ("wgs-8.3" at the time of writing) opens a web page which offers downloads for various operating systems. The "wgs-8.3rc1-Linux_amd64.tar.bz2" file contains a pre-compiled version of PBcR that will work on Abel. In order to download it directly to Abel, click on the "wgs-8.3rc1-Linux_amd64.tar.bz2" file, then right-click on the "direct link" hyperlink and select "copy link location" (you can now terminate the PBcR donwload, if it has started automatically). The direct link to the PBcR download is now available on the clipboard; copy it to Abel so as to download PBcR using the "wget" command.

The following will download and extract the "wgs-8.3" file on Abel:

First, create a folder for PBcR, step into it and download the "wgs-8.3" file:

This downloads a compressed file with a rather long, messy file name:

ls -l

Rename "wgs-8.3rc1-Linux_amd64.tar.bz2\?r\=http\:%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F" to "pbcr.tar.bz2":

mv wgs-8.3rc1-Linux_amd64.tar.bz2\?r\=http\:%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F pbcr.tar.bz2

...and extract the compressed file:

tar xvjf pbcr.tar.bz2

This creates the "wgs-8.3rc1" folder, which contains the PBcR pipeline.

Remove the downloaded compressed file:

rm pbcr.tar.bz2

The installation of PBcR is now complete.

Overview over the installation

Extracting the compressed "pbcr.tar.bz2" file has created the "wgs-8.3rc1" folder, which contains all the files needed for running the PBcR pipeline. This folder contain a readme file and a lincense file, in addition to the "Linux-amd64" folder that contains the PBcR installation:

The "Linux-amd64" folder contains a "bin" folder which contains the individual programs that make up the pipeline. Also, it contains a "lib" folder which holds (amongst other items) the java files that implement the MHAP algorithm needed for the self-correction of PacBio reads. The main PBcR program thus resides in the "Linux-amd64/bin" folder:

Test the installation by executing this program without any input parameters (this displays the help page for PBcR):

./PBcR

Installing the "convertFastaAndQualToFastq.jar" utility

PBcR expects input read files in the fastq format. If reads are available only in fasta format, these may be converted to fastq reads using the "convertFastaAndQualToFastq.jar" utility. This Java script is part of a PBcR tutorial download referred to on the PBcR wiki page: http://wgs-assembler.sourceforge.net/wiki/index.php?title=PBcR#Assembling_a_Lambda_Phage Right-clicking the "Download" hyperlink and selecting "copy link location" will copy the location of the compressed tutorial data folder to the clipboard. On Abel, the following will download and extract the tutorial:

The "sampleData" folder contains the "convertFastaAndQualToFastq.jar" Java script:

Execute the script without any input parameters to read the help file with instructions for use:

java -jar convertFastaAndQualToFastq.jar