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abyss-software [2015/03/16 06:38]
aorth [Abyss]
abyss-software [2019/07/10 14:25] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 1.5.2+  * Version: 2.1.4
   * Added: August, 2013   * Added: August, 2013
-  * Updated: August2014 +  * 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>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.
 +$ 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 6'4.4.x works fine.+There is currently a [[https://github.com/bcgsc/abyss/issues/224|bug in configure's ability to detect the system'OpenMPI]] so we have to set the environment variables manually before building.
abyss-software.1426487885.txt.gz · Last modified: 2015/03/16 06:38 by aorth