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abyss-software [2015/06/10 11:50]
joguya
abyss-software [2019/07/10 14:25] (current)
aorth
Line 4: Line 4:
 ===== Information ===== ===== Information =====
  
-  * Version: 1.9.0+  * Version: 2.1.4
   * Added: August, 2013   * Added: August, 2013
-  * Updated: June2015 +  * 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
  
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 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 ======
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 <code>$ cd /tmp <code>$ cd /tmp
-$ wget https://github.com/bcgsc/abyss/releases/download/1.9.0/abyss-1.9.0.tar.gz +$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz 
-$ tar -xvf abyss-1.9.0.tar.gz +$ tar xf abyss-2.1.4.tar.gz 
-$ cd abyss-1.9.0 +$ cd abyss-2.1.4 
-scl enable devtoolset-2 bash +sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64 
-$ sudo mkdir /export/apps/abyss/1.9.0 +$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64' 
-sudo chown joguya:joguya /export/apps/abyss/1.9.0 +export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi' 
-CC=clang ./configure --prefix=/export/apps/abyss/1.9.0 --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/2.1.4
 +$ sudo chown aorth /export/apps/abyss/2.1.4
 $ make install $ make install
-$ sudo chown -R root:root /export/apps/abyss/1.9.0 +$ sudo chown -R root:root /export/apps/abyss/2.1.4 
-</code>+$ 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.1433937030.txt.gz · Last modified: 2015/06/10 11:50 by joguya