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--- bowtie-software [2014/10/17 07:50] – created joguya
+++ bowtie-software [2015/07/23 09:58] – joguya
@@ Line 2: / Line 2: @@
   * 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 1 =====
+===== Information =====
-==== v1.1.1 ====
-=== Usage ===
-  * show all versions of bowtie<code>$ module avail bowtie
----------------------------------------------------------------------------------------------- /etc/modulefiles/ilri ----------------------------------------------------------------------------------------------
+  * Version: 1.1.2
-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
+  * Added: October, 2014
-</code>
+  * Updated: July, 2015
-  * load a specific version, e.g. v1.1.1: <code>$ module load bowtie/1.1.1</code>
+  * Link: http://bowtie-bio.sourceforge.net/index.shtml
-  * get quick help:<code>$ bowtie --help</code>
-=== Installation ===
+===== Usage =====
-  * 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
+=== See versions of bowtie which are available ===
-set version         1.1.1
+<code>$ module avail bowtie</code>
-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 $msg
+=== Load and run bowtie ===
+<code>$ module load bowtie/1.1.2
+$ bowtie</code>
-proc ModulesHelp { } {
-    puts stderr "$msg"
-}
-conflict        bowtie
+===== Installation ======
+Notes from the sysadmin during installation:
+<code>wget "http://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.1.2/bowtie-1.1.2-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F1.1.2%2F&ts=1437645027&use_mirror=liquidtelecom" -O bowtie-1.1.2-linux-x86_64.zip
+unzip bowtie-1.1.2-linux-x86_64.zip
+cd bowtie-1.1.2
+sudo mkdir /export/apps/bowtie/1.1.2
+sudo cp -r . /export/apps/bowtie/1.1.2/
+</code>
-prepend-path    PATH    ${exec_prefix}</code>
-  * push the new module using ansible<code>ansible-playbook compute.yml --limit=compute --tags=modules -K</code>