Differences

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--- stacks-software [2015/02/05 09:29] – [v1.24] joguya
+++ stacks-software [2023/01/16 07:57] (current) – aorth
@@ Line 2: / Line 2: @@
 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: February, 2015
-  * Added: December, 2014
+  * Updated: January, 2023
-  * Link: http://creskolab.uoregon.edu/stacks/manual/
+  * Link: http://creskolab.uoregon.edu/stacks/manual
 === 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    ${exec_prefix}/bin
-</code>
-  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules</code>
+Notes from the systems administrator during installation:
+<code>$ 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>