Pandaseq

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

Information

• Version: 2.7
• Added: October, 2014
• Link: https://github.com/neufeld/pandaseq/

• module avail pandaseq

• Load pandaseq module:

  module load pandaseq/2.7
  man pandaseq

• 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

Information:

• Version: 2.8.1
• Added: December, 2014
• Link: https://github.com/neufeld/pandaseq/releases/tag/v2.8.1

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

• 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