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stacks-software [2015/02/05 09:27] – created joguyastacks-software [2023/01/16 07:57] (current) aorth
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 Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.
  
-==== v1.24 ==== +  * Version: 2.62 
-  * Version: 1.24 +  * Added: February2015 
-  * Added: December2014 +  * Updated: January, 2023 
-  * Link: http://creskolab.uoregon.edu/stacks/manual/+  * Link: http://creskolab.uoregon.edu/stacks/manual
  
 === Usage === === Usage ===
-  * Show all available versions of stacks<code>module avail stacks</code> 
-  * Load stacks module: <code>module load stacks/1.24</code> 
  
-=== Installation === +Show all available versions:
-  * download stacks tarball & compile it<code>wget http://creskolab.uoregon.edu/stacks/source/stacks-1.24.tar.gz -O stacks-1.24.tar.gz +
-tar -xvf stacks-1.24.tar.gz +
-cd stacks-1.24/ +
-sudo mkdir -p /export/apps/stacks/1.24/ +
-sudo chown -R joguya:joguya /export/apps/stacks/1.24/ +
-./configure --prefix=/export/apps/stacks/1.24/ --enable-bam --with-bam-include-path=/export/apps/samtools/0.1.19/include/bam --with-bam-lib-path=/export/apps/samtools/0.1.19/lib +
-make +
-make install +
-sudo chown -R root:root /export/apps/stacks/1.24/</code> +
-  * stacks module file<code>#%Module1.0 +
-##################################################################### +
-## +
-## stacks Modulefile +
-## By James Oguya, j.oguya@cgiar.org +
-## February, 2015 +
-##+
  
-set appname         stacks +<code>module avail stacks</code>
-set version         1.24 +
-set prefix          /export/apps/${appname}/${version} +
-set exec_prefix     ${prefix} +
-set url "http://creskolab.uoregon.edu/stacks/manual/" +
-set msg "a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.\Stacks Official Site: $url\n"+
  
-module-whatis $msg+Load one version into your environment and run it:
  
-proc ModulesHelp { } { +<code>module load stacks/2.62 
-    puts stderr "$msg" +$ sstacks</code>
-}+
  
-conflict        stacks +=== Installation ===
- +
-prepend-path    PATH    ${exec_prefix}/bin +
-</code>+
  
-  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=module</code>+Notes from the systems administrator during installation:
  
 +<code>$ cd /tmp
 +$ wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.62.tar.gz
 +$ tar xf stacks-2.62.tar.gz
 +$ ./configure --prefix=/export/apps/stacks/2.62
 +$ make
 +$ sudo mkdir -p /export/apps/stacks/2.62
 +$ sudo chown aorth /export/apps/stacks/2.62
 +$ make install</code>
stacks-software.1423128473.txt.gz · Last modified: 2015/02/05 09:27 by joguya