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--- raxml-software [2014/12/08 10:06] – joguya
+++ raxml-software [2018/09/16 07:02] – aorth
@@ Line 1: / Line 1: @@
 ====== 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 =====
+===== Information =====
-==== Information ====
-  * Version: 8.0.23
+  * Latest Version: 8.2.0
   * Added: June, 2011
-  * Updated: May 27, 2014
+  * Updated: July, 2015
   * 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
 rm *.o
 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 ====
-  * Download pandaseq 2.8.1, create version specific dir in /export/apps/pandaseq/, compile & install it.<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
+module load openmpi/1.8.2
+make -f Makefile.MPI.gcc
 rm *.o
-make -f Makefile.AVX.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.PTHREADS.gcc
-rm *.o
-make -f Makefile.AVX.PTHREADS.gcc
-rm *.o
-make -f Makefile.SSE3.PTHREADS.gcc
-rm *.o
-sudo mkdir -p /export/apps/RAxML/8.1.9/bin
-sudo cp raxmlHPC* /export/apps/RAxML/8.1.9/bin/
 </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>