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abyss-software [2015/03/21 16:24]
aorth
abyss-software [2019/07/10 17:25] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 1.5.2+  * Version: ​2.1.4
   * Added: August, 2013   * Added: August, 2013
-  * Updated: ​March2015 +  * 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 ======
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 <​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-2 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'​ 
-/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>​ 
 + 
 +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.1426944282.txt.gz · Last modified: 2015/03/21 16:24 by aorth