Differences

This shows you the differences between two versions of the page.

--- abyss-software [2014/06/10 21:50] – aorth
+++ abyss-software [2018/11/17 20:35] – aorth
@@ Line 1: / Line 1: @@
 ====== Abyss ======
-Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
+Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
 ===== Information =====
-  * Version: 1.5.1
+  * Version: 2.1.4
   * Added: August, 2013
-  * Updated: June 10, 2014
+  * Updated: November, 2018
-  * K-mer size: 64 (default at compile time)
+  * K-mer size: 128 (default at compile time)
   * Link: http://www.bcgsc.ca/platform/bioinfo/software/abyss
 ===== Usage =====
-=== See versions of abyss which are available ===
+See versions of abyss which are available:
-<code>module avail abyss</code>
+<code>$ module avail abyss</code>
+Load one version into your environment and run it:
+<code>$ module load abyss/2.1.4
+$ abyss-pe help</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>wget https://github.com/bcgsc/abyss/releases/download/1.5.1/abyss-1.5.1.tar.gz
+<code>$ cd /tmp
-tar zxf abyss-1.5.1.tar.gz
+$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
-cd abyss-1.5.1
+$ tar xf abyss-2.1.4.tar.gz
-scl enable devtoolset-1.1 bash
+$ cd abyss-2.1.4
-mkdir /tmp/abyss-build
+$ sudo yum install sparsehash-devel.x86_64 openmpi-devel.x86_64
-cd /tmp/abyss-build
+$ ./configure --prefix=/export/apps/abyss/2.1.4
-~/src/abyss-1.5.1/configure --prefix=/export/apps/abyss/1.5.1 --with-boost=/export/apps/boost/1.50.0/include/
+$ make -j4
-sudo mkdir -p /export/apps/abyss/1.5.1
+$ sudo mkdir -p /export/apps/abyss/2.1.4
-sudo chown aorth /export/apps/abyss/1.5.1
+$ sudo chown aorth /export/apps/abyss/2.1.4
-sudo chown -R root:root /export/apps/abyss/1.5.1</code>
+$ make install
+$ sudo chown -R root:root /export/apps/abyss/2.1.4
+$ sudo yum remove sparsehash-devel.x86_64 openmpi-devel.x86_64</code>