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abyss-software [2014/06/10 21:50]
aorth
abyss-software [2019/07/10 14:25] (current)
aorth
Line 1: Line 1:
 ====== Abyss ====== ====== 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 ===== ===== Information =====
  
-  * Version: 1.5.1+  * Version: 2.1.4
   * Added: August, 2013   * Added: August, 2013
-  * Updated: June 102014 +  * Updated: November2018 
-  * 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   * Link: http://www.bcgsc.ca/platform/bioinfo/software/abyss
  
 ===== Usage ===== ===== 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 ====== ===== Installation ======
 Notes from the sysadmin during 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 openmpi3-devel.x86_64 
-cd /tmp/abyss-build +$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64' 
-~/src/abyss-1.5.1/configure --prefix=/export/apps/abyss/1.5.1 --with-boost=/export/apps/boost/1.50.0/include/ +$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi' 
-sudo mkdir -p /export/apps/abyss/1.5.1 +./configure --prefix=/export/apps/abyss/2.1.4 
-sudo chown aorth /export/apps/abyss/1.5.1 +$ make -j4 
-sudo chown -R root:root /export/apps/abyss/1.5.1</code>+sudo mkdir -p /export/apps/abyss/2.1.4 
 +sudo chown aorth /export/apps/abyss/2.1.4 
 +$ make install 
 +sudo chown -R root:root /export/apps/abyss/2.1.
 +$ 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.
abyss-software.1402437024.txt.gz · Last modified: 2014/06/10 21:50 by aorth