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--- velvet-software [2017/09/25 12:25]
aorth [Information]
+++ velvet-software [2017/09/25 12:27] (current)
aorth
@@ Line 12: / Line 12: @@
 ===== Usage =====
-=== See versions of velvet which are available ===
+See versions of velvet which are available:
-<code>module avail velvet</code>
+<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.
 === Extra information ===
@@ Line 28: / Line 21: @@
 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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