Differences

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--- muscle-software [2014/08/11 13:11] – joguya
+++ muscle-software [2023/02/23 06:10] (current) – aorth
@@ Line 1: / Line 1: @@
-====== Muscle ======
+====== MUSCLE ======
-  * Version 3.8.31
+MUSCLE is a multiple alignment program with accuracy and speed that are consistently better than CLUSTALW.
-  * Added August, 2014
-  * Link [[http://www.drive5.com/muscle]]
-  * One of the scientist requested us to add a new module known as [[http://www.mybiosoftware.com/alignment/1284|muscle]] for amino acids alignment.
-  * Download muscle binaries, in /export/apps/, create muscle/ folder & in it create muscle_version_number in this case it would be 3.8.31.
-  * Copy over the binaries to /export/apps/muscle/muscle_version_number/ i.e. **/export/apps/muscle/3.8.31/**
-  * Clone [[https://github.com/ilri/hpc-environment-modules|hpc-environment-modules]] from github
-  * cd to hpc-environment-modules git repo & mkdir muscle, in it create the module file & name it the version number i.e. 3.8.31
-  * Commit & push to github
-  * Run ansible & limit to compute nodes & modules tag
-<code>
-ssh hpc
-wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
-tar -xvf muscle3.8.31_i86linux64.tar.gz
-sudo su -
-mkdir -p /export/apps/muscle/3.8.31
-cp muscle /export/apps/muscle/3.8.31/
-</code>
-  * Clone environment modules & add a new module
+===== Information =====
-<code>
+  * Version: 3.8.1551
-git clone https://github.com/ilri/hpc-environment-modules.git
+  * Added: April, 2020
-cd hpc-environment-modules/
+  * Updated: February, 2023
-mkdir muscle/
+  * Link: http://www.drive5.com/muscle/
-vim muscle/3.8.31
-</code>
-  * Muscle module file
+===== Usage =====
-<file>
+See versions of muscle which are available:
-#%Module1.0#####################################################################
+<code>$ module avail muscle</code>
-##
-## Muscle modulefile
-## By James Oguya <j.oguya@cgiar.org>
-## August, 2014
-##
-module-whatis "muscle is a program for creating multiple alignments of amino acid or nucleotide sequences"
+Load a particular version into your environment and run it:
-# for TCL script use
+<code>$ module load muscle/3.8.1551
-set     version         3.8.31
+$ muscle -version
-set     appname         muscle
+MUSCLE v3.8.1551 by Robert C. Edgar</code>
-set     prefix          /export/apps/${appname}/${version}
-set     exec_prefix     ${prefix}
-prepend-path    PATH            ${exec_prefix}
+===== Installation ======
-</file>
+Notes from the sysadmin during installation:
-  * Deploy new module using ansible
+<code>$ cd /tmp
+$ wget http://www.drive5.com/muscle/muscle_src_3.8.1551.tar.gz
+$ mkdir muscle
+$ tar xf muscle_src_3.8.1551.tar.gz -C muscle
+$ cd muscle
+$ sudo dnf install glibc-static libstdc++-static.x86_64
+$ make
+$ sudo mkdir -p /export/apps/muscle/3.8.1551
+$ sudo cp muscle /export/apps/muscle/3.8.1551</code>
-<code>
+If you get an error about inability to link against ''-lm'' you need to install ''glibc-static''.
-ansible-playbook site.yml -i private/hosts --limit compute --tags=modules -u joguya -K
-</code>
-  * Test to confirm success: do a module avail, module load muscle/3.8.31, muscle
-<code>
-module avail
-module load muscle/3.8.31
-module ls
-muscle
-module unload
-</code>