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muscle-software [2014/08/11 13:11]
joguya
muscle-software [2020/04/16 09:47] (current)
aorth
Line 1: Line 1:
-====== Muscle ====== +====== MUSCLE ====== 
-  * Version 3.8.31 +MUSCLE is 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 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> +  * Version3.8.1551 
-git clone https://github.com/ilri/hpc-environment-modules.git +  * Added: April, 2020,  
-cd hpc-environment-modules/ +  * Link: http://www.drive5.com/muscle/
-mkdir 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 program for creating multiple alignments of amino acid or nucleotide sequences"+Load 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 yum install glibc-static 
 +$ scl enable devtoolset-7 bash 
 +$ 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 ''glib-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>+
muscle-software.1407762704.txt.gz · Last modified: 2014/08/11 13:11 by joguya