Difference between revisions of "PBcR: Installation"
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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. | ||
+ | |||
= Installing PBcR on Abel = | = 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/] | [http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/ 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. | + | 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 " | + | 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;"> | ||
mkdir PBcR | mkdir 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&ts=1429873744&use_mirror=cznic] | 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&ts=1429873744&use_mirror=cznic] | ||
− | + | </div> | |
This downloads a compressed file with a rather long, messy file name: | This downloads a compressed file with a rather long, messy file name: | ||
− | ls -l | + | <span style="font-family:courier new,courier,monospace;">ls -l</span> |
− | 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": | + | 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>": |
− | 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 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> |
...and extract the compressed file: | ...and extract the compressed file: | ||
− | tar xvjf pbcr.tar.bz2 | + | <span style="font-family:courier new,courier,monospace;">tar xvjf pbcr.tar.bz2</span> |
− | This creates the "wgs-8.3rc1" folder, which contains the PBcR pipeline. | + | 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: | Remove the downloaded compressed file: | ||
− | rm pbcr.tar.bz2 | + | <span style="font-family:courier new,courier,monospace;">rm pbcr.tar.bz2</span> |
The installation of PBcR is now complete. | The installation of PBcR is now complete. | ||
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= Overview over the installation = | = 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: | + | 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: |
− | + | <div style="line-height:90%; background-color: LightGray; border-style: solid; border-width:1px; font-family:courier new,courier,monospace;"> | |
cd wgs-8.3rc1 | cd wgs-8.3rc1 | ||
ls -l | ls -l | ||
− | + | </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. The main PBcR program thus resides in the "Linux-amd64/bin" folder: | + | 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 Linux-amd64/ | ||
Line 52: | Line 54: | ||
ls -l | ls -l | ||
− | + | </div> | |
Test the installation by executing this program without any input parameters (this displays the help page for PBcR): | Test the installation by executing this program without any input parameters (this displays the help page for PBcR): | ||
− | ./PBcR | + | <span style="font-family:courier new,courier,monospace;">./PBcR</span> |
− | = Installing the "convertFastaAndQualToFastq.jar" utility | + | = 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 "convertFastaAndQualToFastq.jar" utility. This Java script is part of a PBcR tutorial download referred to on the PBcR wiki page | + | 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] | |
− | tar | + | 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] | ||
− | The "sampleData" folder contains the "convertFastaAndQualToFastq.jar" Java script: | + | 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> | |
− | ls -l | + | Execute the script without any input parameters to read the help file with instructions for use: |
− | |||
− | Execute the script without any input parameters to read the help file with instructions for use: | ||
− | java -jar convertFastaAndQualToFastq.jar | + | <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:
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