Differences

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--- velvet-software [2014/05/27 09:59] – [Usage] aorth
+++ velvet-software [2017/09/25 12:26] – [Usage] aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Added: November 15, 2012
+  * Version: 1.2.10-kmer111
-  * Updated: May 27, 2014
+  * MAXKMERLENGTH: 111
+  * Added: November, 2012
+  * Updated: September, 2017
   * Link: https://www.ebi.ac.uk/~zerbino/velvet/
 ===== Usage =====
-See versions of velvet:
-<code>module avail velvet</code>
+See versions of velvet which are available:
+<code>$ module avail velvet</code>
+=== Memory Estimating ===
+The following tool may be helpful in estimating memory requirements for your velvet run:
+  * http://denovoutils.appspot.com/velvetmem
+Make sure you substitute in the correct value for "k" based on the ''MAXKMERLENGTH'' used in your Velvet build (see information above).
+=== Extra information ===
+  * https://wiki.hpcc.msu.edu/display/Bioinfo/Velvet+and+Oases
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code></code>
+<code>$ cd /tmp
+$ wget wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
+$ tar xf velvet_1.2.10.tgz
+$ cd velvet_1.2.10
+$ scl enable devtoolset-4 bash
+$ sed -i 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=111/' Makefile
+$ make OPENMP=1
+$ make cleanobj
+$ sudo cp -r . /export/apps/velvet/1.2.10-kmer111</code>