Differences

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--- velvet-software [2014/05/27 10:02]
aorth [Installation]
+++ velvet-software [2017/09/25 12:27] (current)
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 which are available:
-<code>module avail velvet</code>
+<code>$ module avail velvet</code>
+=== Extra information ===
+  * https://wiki.hpcc.msu.edu/display/Bioinfo/Velvet+and+Oases
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
+<code>$ cd /tmp
-tar xf velvet_1.2.10.tgz
+$ wget wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
-cd velvet_1.2.10
+$ tar xf velvet_1.2.10.tgz
-scl enable devtoolset-1.1 bash
+$ cd velvet_1.2.10
-sed 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=64/' Makefile > Makefile.kmer64
+$ scl enable devtoolset-4 bash
-make -f Makefile.kmer64
+$ sed -i 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=111/' Makefile
-make -f Makefile.kmer64 cleanobj
+$ make OPENMP=1
-sudo cp -r . /export/apps/velvet/1.2.10-kmer64</code>
+$ make cleanobj
+$ sudo cp -r . /export/apps/velvet/1.2.10-kmer111</code>

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