Differences

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--- abyss-software [2014/08/28 10:11] – aorth
+++ abyss-software [2019/07/10 14:25] (current) – 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: 1.5.2
+  * Version: 2.1.4
   * Added: August, 2013
-  * Updated: August, 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>cd /tmp
+<code>$ cd /tmp
-wget https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz
+$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
-tar xf abyss-1.5.2.tar.gz
+$ tar xf abyss-2.1.4.tar.gz
-cd abyss-1.5.2
+$ cd abyss-2.1.4
-scl enable devtoolset-1.1 bash
+$ sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64
-mkdir /tmp/abyss-build
+$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
-cd /tmp/abyss-build
+$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
-LIBS="-lpthread" /tmp/abyss-1.5.2/configure --prefix=/export/apps/abyss/1.5.2 --with-boost=/export/apps/boost/1.50.0/include --with-mpi=/export/apps/openmpi/1.8.2
+$ ./configure --prefix=/export/apps/abyss/2.1.4
-make -j4
+$ make -j4
-sudo mkdir -p /export/apps/abyss/1.5.2
+$ sudo mkdir -p /export/apps/abyss/2.1.4
-sudo chown aorth /export/apps/abyss/1.5.2
+$ sudo chown aorth /export/apps/abyss/2.1.4
-make install
+$ make install
-sudo chown -R root:root /export/apps/abyss/1.5.2</code>
+$ sudo chown -R root:root /export/apps/abyss/2.1.4
+$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64</code>
-**Note:** Seems to have a problem compiling with GCC 4.7.2 when you don't specify the extra LIBS.  CentOS 6's 4.4.x works fine.
+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.