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muscle-software [2014/08/11 13:06]
joguya created
muscle-software [2020/04/16 09:47]
aorth
Line 1: Line 1:
-====== ​Muscle ​====== +====== ​MUSCLE ​====== 
-  * One of the scientist requested us to add new module known as [[http://​www.mybiosoftware.com/​alignment/​1284|muscle]] for amino acids alignment. +MUSCLE is multiple ​alignment ​program with accuracy and speed that are consistently better than CLUSTALW.
-  * 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.txt · Last modified: 2020/04/16 09:47 by aorth