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pandaseq-software

Pandaseq

Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Pandaseq 2.7

Information

Usage

Show available version

  • module avail pandaseq

Show manpages

  • Load pandaseq module:
    module load pandaseq/2.7
    man pandaseq

Installation

  • clone repo from github
    cd /home/joguya/src
    git clone https://github.com/neufeld/pandaseq.git
    cd pandaseq
  • generate configs files
    ./autogen.sh
  • create the directory(/export/apps/pandaseq/2.7) where we're going to install pandaseq:
    sudo mkdir -p /export/apps/pandaseq/2.7/
    sudo chown joguya:joguya /export/apps/pandaseq/2.7 
  • run configure script & provide the prefix(installation target dir)
    ./configure --prefix=/export/apps/pandaseq/2.7/
  • create make file & install
    make
    make install 
  • change ownership back to root
    sudo chown -R root:root /export/apps/pandaseq/2.7/
  • module file for version 2.7
    #%Module1.0#####################################################################
    ##
    ## pandaseq modulefile 
    ## By James Oguya <j.oguya@cgiar.org>
    ## October, 2014
    ##
    
    module-whatis "pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence."
    
    # for Tcl script use only
    set     appname         pandaseq
    set     version         2.7
    set     prefix          /export/apps/${appname}/${version}
    set     exec_prefix     ${prefix}/bin
    set     datarootdir     ${prefix}/share
    
    conflict        pandaseq
    
    prepend-path    PATH            ${exec_prefix}
    prepend-path    MANPATH         ${datarootdir}/man
  • deploy the new module using ansible
    ansible-playbook site.yml -u joguya -K -s --limit=compute --tags=module
  • do a quick module load/unload to perform a quick test
    module load pandaseq/2.7
    pandaseq -h
    man pandaseq

Pandaseq 2.8.1

Information:

changelog:

  • Add a plugin to display overlaps examined
  • Add -D flag to add a penalty for shifting primers
  • Added UPARSE algorithm
  • Add FastqJoin algorithm
  • Add FLASH algorithm
  • Add Sitch algorithm
  • Fix bug causing spurious "no sequences" with one thread
  • Issue an error if the command line arguments have UTF-8 characters
  • Remove min_readqscore since it doesn't work as advertised
  • Sanity check sequence length after primer stripping

Installation Notes

  • Download pandaseq 2.8.1, create version specific dir in /export/apps/pandaseq/, compile & install it.
    wget https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz -O pandaseq-v2.8.1.tar.gz
    tar -xvf pandaseq-v2.8.1.tar.gz
    cd pandaseq-v2.8.1
    sudo mkdir /export/apps/pandaseq/2.8.1/
    sudo chown -R joguya:joguya /export/apps/pandaseq/2.8.1
    ./autogen.sh
    ./configure --prefix=/export/apps/pandaseq/2.8.1
    make
    make install
    sudo chown -R root:root /export/apps/pandaseq/2.8.1
  • pandaseq/2.8.1 module file:
    #%Module1.0
    #####################################################################
    ##
    ## Pandaseq Modulefile
    ## By James Oguya, j.oguya@cgiar.org
    ## December, 2014
    ##
    
    set appname         pandaseq
    set version         2.8.1
    set prefix          /export/apps/${appname}/${version}
    set exec_prefix     ${prefix}/bin
    set url "https://github.com/neufeld/pandaseq/"
    set msg "pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.\nPandaseq Official Site: $url\n"
    
    module-whatis $msg
    
    proc ModulesHelp { } {
        puts stderr "$msg"
    }
    
    conflict        pandaseq
    
    prepend-path    PATH        ${exec_prefix}
    prepend-path    MANPATH     ${prefix}/share/man
pandaseq-software.txt · Last modified: 2014/12/08 12:27 by joguya