ILRI Research Computing

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====== Bowtie ======
  * Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
  * For reads longer than about 50 bp Bowtie 2 is generally faster, more sensitive, and uses less memory than Bowtie 1. For relatively short reads (e.g. less than 50 bp) Bowtie 1 is sometimes faster and/or more sensitive.
  * There is no upper limit on read length in Bowtie 2. Bowtie 1 had an upper limit of around 1000 bp.
  * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#how-is-bowtie-2-different-from-bowtie-1| differences between Bowtie1 & Bowtie2]]

===== Bowtie v1.1.1 =====
==== Usage ====
  * show all versions of bowtie<code>$ module avail bowtie

---------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
bowtie/0.12.7 bowtie/0.12.8 bowtie/1.0.0  bowtie/1.0.1  bowtie/1.1.1  bowtie2/2.1.0 bowtie2/2.2.2 bowtie2/2.2.3
</code>
  * load a specific version, e.g. v1.1.1: <code>$ module load bowtie/1.1.1</code>
  * get quick help:<code>$ bowtie --help</code>

==== Installation ====
  * bowtie comes already compiled, so all you have to do is unzip & copy to export-apps<code>wget "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F1.1.1%2F&ts=1413524287&use_mirror=tenet" -O bowtie-1.1.1-linux-x86_64.zip
unzip bowtie-1.1.1-linux-x86_64.zip
sudo mkdir /export/apps/bowtie/1.1.1/
sudo cp -r bowtie-1.1.1/* /export/apps/bowtie/1.1.1/
</code>
  * create module file:<code>#%Module1.0
#####################################################################
##
## bowtie Modulefile
## By James Oguya, j.oguya@cgiar.org
## October, 2014
##

set appname         bowtie
set version         1.1.1
set prefix          /export/apps/${appname}/${version}
set exec_prefix     ${prefix}
set url "http://bowtie-bio.sourceforge.net"
set msg "bowtie is an ultrafast, memory-efficient short read aligner that aligns DNA sequences(reads) to the human at 25 million 35-bp reads per hour.\nBowtie Official Site: $url\n"

module-whatis $msg

proc ModulesHelp { } {
    puts stderr "$msg"
}

conflict        bowtie

prepend-path    PATH    ${exec_prefix}</code>
  * push the new module using ansible<code>ansible-playbook compute.yml --limit=compute --tags=modules -K</code>