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


==== Usage ====

=== Show available version ===

  * <code>module avail pandaseq</code>


=== Show manpages === 
  * Load pandaseq module: <code>module load pandaseq/2.7
man pandaseq</code>


==== Installation ====
  * clone repo from [[https://github.com/neufeld/pandaseq.git|github]] <code>cd /home/joguya/src
git clone https://github.com/neufeld/pandaseq.git
cd pandaseq</code>
  * generate configs files <code>./autogen.sh</code>
  * create the directory(/export/apps/pandaseq/2.7) where we're going to install pandaseq:<code>sudo mkdir -p /export/apps/pandaseq/2.7/
sudo chown joguya:joguya /export/apps/pandaseq/2.7 </code>
  * run configure script & provide the prefix(installation target dir)<code>./configure --prefix=/export/apps/pandaseq/2.7/</code>
  * create make file & install <code>make
make install </code>
  * change ownership back to root<code>sudo chown -R root:root /export/apps/pandaseq/2.7/</code>
  * module file for version 2.7<code>
#%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
</code>

  * deploy the new module using ansible<code>ansible-playbook site.yml -u joguya -K -s --limit=compute --tags=module</code>
  * do a quick module load/unload to perform a quick test<code>module load pandaseq/2.7
pandaseq -h
man pandaseq
</code>

===== Pandaseq 2.8.1 =====
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


==== Installation Notes ====
  * Download pandaseq 2.8.1, create version specific dir in /export/apps/pandaseq/, compile & install it.<code>
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
</code>

  * pandaseq/2.8.1 module file:<code>
#%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
</code>