Difference between revisions of "PBcR: Installation"

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(Created page with "<div>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 ut...")
 
 
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<div>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.</div><div><br/></div>
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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.&nbsp;
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= Installation of the PBcR pipeline =
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<div><br/></div><div>PBcR can be downloaded from the "Whole-Genome Shotgun Assembler" sourceforge web page:</div><div><br/></div><div>http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/</div><div><br/></div><div>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.</div><div>The following will download and extract the "wgs-8.3" file on Abel:</div><div><br/></div><div>First, create a folder for PBcR, step into it and download the "wgs-8.3" file:</div><div>mkdir PBcR</div><div>cd PBcR</div><div>wget http://downloads.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-8.3/wgs-8.3rc1-Linux_amd64.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F&ts=1429873744&use_mirror=cznic</div><div><br/></div><div>This downloads a compressed file with a rather long, messy file name:</div><div><br/></div><div>ls -l</div><div><br/></div><div>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":</div><div><br/></div><div>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</div><div>...and extract the compressed file:</div><div>tar xvjf pbcr.tar.bz2</div><div><br/></div><div>This creates the "wgs-8.3rc1" folder, which contains the PBcR pipeline. Remove the downloaded compressed file:</div><div><br/></div><div>rm pbcr.tar.bz2</div><div><br/></div><div>The installation of PBcR is now complete.</div><div><br/></div>
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= Installing PBcR on Abel =
 +
 
 +
PBcR can be downloaded from the "Whole-Genome Shotgun Assembler" sourceforge web page:
 +
 
 +
[http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/]
 +
 
 +
Clicking on the current version ("<span style="font-family:courier new,courier,monospace;">wgs-8.3</span>" at the time of writing) opens a web page which offers downloads for various operating systems. The "<span style="font-family:courier new,courier,monospace;">wgs-8.3rc1-Linux_amd64.tar.bz2</span>" file contains a pre-compiled version of PBcR that will work on Abel. In order to download it directly to Abel, click on the "<span style="font-family:courier new,courier,monospace;">wgs-8.3rc1-Linux_amd64.tar.bz2</span>" 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 "<span style="font-family:courier new,courier,monospace;">wget</span>" command.
 +
 
 +
The following will download and extract the "<span style="font-family:courier new,courier,monospace;">wgs-8.3"</span> file on Abel:
 +
 
 +
First, create a folder for PBcR, step into it and download the "<span style="font-family:courier new,courier,monospace;">wgs-8.3</span>" file:
 +
<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;">
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mkdir PBcR
 +
 
 +
cd PBcR
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 +
wget [http://downloads.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-8.3/wgs-8.3rc1-Linux_amd64.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F&ts=1429873744&use_mirror=cznic http://downloads.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-8.3/wgs-8.3rc1-Linux_amd64.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F&amp;ts=1429873744&amp;use_mirror=cznic]
 +
</div>
 +
This downloads a compressed file with a rather long, messy file name:
 +
 
 +
<span style="font-family:courier new,courier,monospace;">ls -l</span>
 +
 
 +
Rename "<span style="font-family:courier new,courier,monospace;">wgs-8.3rc1-Linux_amd64.tar.bz2\?r\=http\:%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F</span>" to "<span style="font-family:courier new,courier,monospace;">pbcr.tar.bz2</span>":
 +
 
 +
<span style="font-family:courier new,courier,monospace;">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</span>
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 +
...and extract the compressed file:
 +
 
 +
<span style="font-family:courier new,courier,monospace;">tar xvjf pbcr.tar.bz2</span>
 +
 
 +
This creates the "<span style="font-family:courier new,courier,monospace;">wgs-8.3rc1</span>" folder, which contains the PBcR pipeline.
 +
 
 +
Remove the downloaded compressed file:
 +
 
 +
<span style="font-family:courier new,courier,monospace;">rm pbcr.tar.bz2</span>
 +
 
 +
The installation of PBcR is now complete.
 +
 
 
= Overview over the installation =
 
= Overview over the installation =
−
<div>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.&nbsp;</div><div>This folder contain a readme file and a lincense file, in addition to the "Linux-amd64" folder that contains the PBcR installation:</div><div><br/></div><div>cd wgs-8.3rc1</div><div>ls -l</div><div><br/></div><div>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.</div><div>The main PBcR program thus resides in the "Linux-amd64/bin" folder:</div><div><br/></div><div>cd Linux-amd64/</div><div>cd bin</div><div>ls -l</div><div><br/></div><div>Test the installation by executing this program without any input parameters (this displays the help page for PBcR):</div><div><br/></div><div>./PBcR</div><div><br/></div>
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= Installing the "convertFastaAndQualToFastq.jar" utility =
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Extracting the compressed "<span style="font-family:courier new,courier,monospace;">pbcr.tar.bz2</span>" file has created the "<span style="font-family:courier new,courier,monospace;">wgs-8.3rc1</span>" 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 "<span style="font-family:courier new,courier,monospace;">Linux-amd64</span>" folder that contains the PBcR installation:
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<div><br/></div><div>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:</div><div><br/></div><div>http://wgs-assembler.sourceforge.net/wiki/index.php?title=PBcR#Assembling_a_Lambda_Phage</div><div><br/></div><div>Right-clicking the "Download" hyperlink and selecting "copy link location" will copy the location of the compressed tutorial data folder to the clipboard.</div><div>On Abel, the following will download and extract the tutorial:</div><div><br/></div><div>wget http://www.cbcb.umd.edu/software/PBcR/data/sampleData.tar.gz</div><div>tar xzvf sampleData.tar.gz</div><div><br/></div><div>The "sampleData" folder contains the "convertFastaAndQualToFastq.jar" Java script:</div><div><br/></div><div>cd sampleData/</div><div>ls -l</div><div><br/></div><div>Execute the script without any input parameters to read the help file with instructions for use:</div><div><br/></div><div>java -jar convertFastaAndQualToFastq.jar</div>
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<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;">
 +
cd wgs-8.3rc1
 +
 
 +
ls -l
 +
</div>
 +
The "<span style="font-family:courier new,courier,monospace;">Linux-amd64</span>" folder contains a "<span style="font-family:courier new,courier,monospace;">bin</span>" folder which contains the individual programs that make up the pipeline. Also, it contains a "<span style="font-family:courier new,courier,monospace;">lib</span>" 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 "<span style="font-family:courier new,courier,monospace;">Linux-amd64/bin</span>" folder:
 +
<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;">
 +
cd Linux-amd64/
 +
 
 +
cd bin
 +
 
 +
ls -l
 +
</div>
 +
Test the installation by executing this program without any input parameters (this displays the help page for PBcR):
 +
 
 +
<span style="font-family:courier new,courier,monospace;">./PBcR</span>
 +
 
 +
= Installing the "<span style="font-family:courier new,courier,monospace;">convertFastaAndQualToFastq.jar</span>" 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 "<span style="font-family:courier new,courier,monospace;">convertFastaAndQualToFastq.jar</span>" 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 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:
 +
<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;">
 +
wget [http://www.cbcb.umd.edu/software/PBcR/data/sampleData.tar.gz http://www.cbcb.umd.edu/software/PBcR/data/sampleData.tar.gz]
 +
 
 +
tar xzvf sampleData.tar.gz
 +
</div>
 +
The "<span style="font-family:courier new,courier,monospace;">sampleData</span>" folder contains the "<span style="font-family:courier new,courier,monospace;">convertFastaAndQualToFastq.jar</span>" Java script:
 +
<div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;">
 +
cd sampleData/
 +
 
 +
ls -l
 +
</div>
 +
Execute the script without any input parameters to read the help file with instructions for use:
 +
 
 +
<span style="font-family:courier new,courier,monospace;">java -jar convertFastaAndQualToFastq.jar</span>

Latest revision as of 14:46, 24 April 2015

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. 

Installing PBcR on Abel

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:

mkdir PBcR

cd PBcR

wget http://downloads.sourceforge.net/project/wgs-assembler/wgs-assembler/wgs-8.3/wgs-8.3rc1-Linux_amd64.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwgs-assembler%2Ffiles%2Fwgs-assembler%2Fwgs-8.3%2F&ts=1429873744&use_mirror=cznic

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:

cd wgs-8.3rc1

ls -l

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:

cd Linux-amd64/

cd bin

ls -l

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:

wget http://www.cbcb.umd.edu/software/PBcR/data/sampleData.tar.gz

tar xzvf sampleData.tar.gz

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

cd sampleData/

ls -l

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

java -jar convertFastaAndQualToFastq.jar

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