Differences

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

--- abyss-software [2017/10/14 13:37] – aorth
+++ abyss-software [2019/07/10 14:25] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 2.0.2
+  * Version: 2.1.4
   * Added: August, 2013
-  * Updated: October, 2017
+  * 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
@@ Line 16: / Line 16: @@
 Load one version into your environment and run it:
-<code>$ module load abyss/2.0.2
+<code>$ module load abyss/2.1.4
-$ abyss-pe --help</code>
+$ abyss-pe help</code>
 ===== Installation ======
@@ Line 23: / Line 23: @@
 <code>$ cd /tmp
-$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz
+$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
-$ tar xf abyss-2.0.2.tar.gz
+$ tar xf abyss-2.1.4.tar.gz
-$ cd abyss-2.0.2
+$ cd abyss-2.1.4
-$ scl enable devtoolset-4 bash
+$ sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64
-$ ./configure --prefix=/export/apps/abyss/2.0.2 --with-boost=/export/apps/boost/1.65.1/include --with-mpi=/export/apps/openmpi/1.8.2
+$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
+$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
+$ ./configure --prefix=/export/apps/abyss/2.1.4
 $ make -j4
-$ sudo mkdir /export/apps/abyss/2.0.2
+$ sudo mkdir -p /export/apps/abyss/2.1.4
-$ sudo chown aorth /export/apps/abyss/2.0.2
+$ sudo chown aorth /export/apps/abyss/2.1.4
 $ make install
-$ sudo chown -R root:root /export/apps/abyss/2.0.2</code>
+$ sudo chown -R root:root /export/apps/abyss/2.1.4
+$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64</code>
+There is currently a [[https://github.com/bcgsc/abyss/issues/224|bug in configure's ability to detect the system's OpenMPI]] so we have to set the environment variables manually before building.