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raxml-software [2014/12/08 13:24]
joguya [Installation Notes]
raxml-software [2015/07/27 10:18] (current)
joguya
Line 1: Line 1:
 ====== RAxML ====== ====== RAxML ======
 +RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. ​
  
-===== RAxML 8.0.23 ===== +  ​Latest ​Version: 8.2.0
-==== Information ==== +
- +
-  ​* Version: 8.0.23+
   * Added: June, 2011   * Added: June, 2011
-  * Updated: ​May 272014+  * Updated: ​July2015
   * Link: https://​github.com/​stamatak/​standard-RAxML   * Link: https://​github.com/​stamatak/​standard-RAxML
  
-==== Usage ====+=== Usage === 
 +  * Show all available versions of RAxML<​code>​module avail RAxML</​code>​ 
 +  * Load RAxML module: <​code>​module load RAxML/​8.2.0</​code>​
  
-=== See versions of RAxML which are available === +=== Installation === 
-<​code>​module avail RAxML</​code>​ +  *Notes from the sysadmin during installation:<​code>​ 
- +wget https://​github.com/​stamatak/​standard-RAxML/archive/v8.2.0.tar.gz 
-==== Installation ​===== +tar -xvf v8.2.0.tar.gz 
-Notes from the sysadmin during installation:​ +cd standard-RAxML-8.2.0/
- +
-<​code>​git clone https://​github.com/​stamatak/​standard-RAxML.git +
-cd standard-RAxML +
-scl enable devtoolset-1.1 bash +
-git checkout v8.0.23+
 make -f Makefile.AVX.gcc make -f Makefile.AVX.gcc
 rm *.o rm *.o
 make -f Makefile.AVX.PTHREADS.gcc make -f Makefile.AVX.PTHREADS.gcc
-sudo mkdir -p /​export/​apps/​RAxML/​8.0.23/​bin 
-sudo cp raxmlHPC-* /​export/​apps/​RAxML/​8.0.23/​bin/</​code>​ 
-===== RAxML 8.1.9 ===== 
-Information:​ 
-  * Version: 8.1.9 
-  * Added: December, 2014 
-  * Link: https://​github.com/​stamatak/​standard-RAxML/​releases/​tag/​v8.1.9 
- 
-==== Installation Notes ==== 
-  * clone RAxML GitHub repo, create version specific dir in /​export/​apps/​RAxML/,​ compile & copy binaries<​code>​ 
-git clone https://​github.com/​stamatak/​standard-RAxML.git 
-cd standard-RAxML 
-scl enable devtoolset-1.1 bash 
-git checkout v8.1.9 
-make -f Makefile.gcc 
-rm *.o 
-make -f Makefile.SSE3.gcc 
-rm *.o 
-make -f Makefile.AVX.gcc 
-rm *.o 
-make -f Makefile.PTHREADS.gcc 
-rm *.o 
-make -f Makefile.AVX.PTHREADS.gcc 
-rm *.o 
-make -f Makefile.SSE3.PTHREADS.gcc 
 rm *.o rm *.o
 module load openmpi/​1.8.2 module load openmpi/​1.8.2
 make -f Makefile.MPI.gcc make -f Makefile.MPI.gcc
 rm *.o rm *.o
-make -f Makefile.SSE3.MPI.gcc +sudo mkdir -p /​export/​apps/​RAxML/​8.2.0/bin 
-rm *.o +sudo cp -v raxmlHPC* /​export/​apps/​RAxML/​8.2.0/bin/
-make -f Makefile.AVX.MPI.gcc +
-rm *.o +
-sudo mkdir -p /​export/​apps/​RAxML/​8.1.9/bin +
-sudo cp raxmlHPC* /​export/​apps/​RAxML/​8.1.9/bin/+
 </​code>​ </​code>​
- 
-  * RAxML/8.1.9 module file:<​code>#​%Module1.0 
-#####################################################################​ 
-## 
-## RAxML Modulefile 
-## by James Oguya, <​j.oguya@cgiar.org>​ 
-## December, 2014 
-## 
- 
-set     ​appname ​        RAxML 
-set     ​version ​        8.1.9 
-set     ​prefix ​         /​export/​apps/​${appname}/​${version} 
-set     ​exec_prefix ​    ​${prefix}/​bin 
- 
-conflict ​   RAxML 
- 
-prepend-path ​   PATH            ${exec_prefix} 
-</​code>​ 
- 
- 
raxml-software.txt · Last modified: 2015/07/27 10:18 by joguya