Differences

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--- velvet-software [2014/05/27 10:23] – [Usage] aorth
+++ velvet-software [2025/05/06 08:52] (current) – aorth
@@ Line 5: / Line 5: @@
   * Version: 1.2.10
-  * MAXKMERLENGTH: 31
+  * Added: November, 2012
-  * Added: November 15, 2012
+  * Updated: May, 2025
-  * Updated: May 27, 2014
+  * Link: https://github.com/dzerbino/velvet
-  * Link: https://www.ebi.ac.uk/~zerbino/velvet/
 ===== Usage =====
-See versions of velvet which are available:
-<code>module avail velvet</code>
-=== Memory Estimating ===
+See versions which are available:
+<code>$ module avail velvet</code>
-The following tool may be helpful in estimating memory requirements for your velvet run:
+Load one version into your environment and run it:
-  * http://denovoutils.appspot.com/velvetmem
+<code>$ module load velvet/1.2.10
+$ velvetg</code>
-Make sure you substitute in the correct value for "k" based on the MAXKMERLENGTH used in your Velvet build.
 === Extra information ===
@@ Line 27: / Line 24: @@
 Notes from the sysadmin during installation:
-<code>wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
+<code>$ wget https://github.com/dzerbino/velvet/archive/refs/tags/v1.2.10.tar.gz
-tar xf velvet_1.2.10.tgz
+$ tar xf v1.2.10.tar.gz
-cd velvet_1.2.10
+$ cd velvet-1.2.10
-scl enable devtoolset-1.1 bash
+$ make OPENMP=1
-sed 's/MAXKMERLENGTH=[0-9].*$/MAXKMERLENGTH=64/' Makefile > Makefile.kmer64
+$ make cleanobj
-make -f Makefile.kmer64
+$ sudo cp -r . /export/apps/velvet/1.2.10</code>
-make -f Makefile.kmer64 cleanobj
-sudo cp -r . /export/apps/velvet/1.2.10-kmer64</code>