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abyss-software [2017/10/14 16:39]
aorth
abyss-software [2019/07/10 17:25]
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 2.0.2+  * Version: 2.1.4
   * Added: August, 2013   * Added: August, 2013
-  * Updated: ​October2017 +  * 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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 Load one version into your environment and run it: Load one version into your environment and run it:
-<​code>​$ module load abyss/2.0.2+<​code>​$ module load abyss/2.1.4
 $ abyss-pe help</​code>​ $ abyss-pe help</​code>​
  
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 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget http://​www.bcgsc.ca/​platform/​bioinfo/​software/​abyss/​releases/​2.0.2/abyss-2.0.2.tar.gz +$ wget http://​www.bcgsc.ca/​platform/​bioinfo/​software/​abyss/​releases/​2.1.4/abyss-2.1.4.tar.gz 
-$ tar xf abyss-2.0.2.tar.gz  +$ tar xf abyss-2.1.4.tar.gz 
-$ cd abyss-2.0.2 +$ cd abyss-2.1.4 
-scl enable devtoolset-4 bash +sudo yum install sparsehash-devel.x86_64 openmpi3-devel.x86_64 
-./​configure ​--prefix=/export/apps/abyss/2.0.2 --with-boost=/export/apps/boost/1.65.1/include --with-mpi=/​export/​apps/​openmpi/1.8.2+export CPPFLAGS='​-pthread ​-I/usr/​include/​openmpi3-x86_64'​ 
 +export ​LIBS='​-Wl,​-rpath -Wl,/usr/lib64/openmpi3/​lib ​-Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'​ 
 +./configure ​--prefix=/​export/​apps/​abyss/2.1.4
 $ make -j4 $ make -j4
-$ sudo mkdir /​export/​apps/​abyss/​2.0.2 +$ sudo mkdir -p /​export/​apps/​abyss/​2.1.4 
-$ sudo chown aorth /​export/​apps/​abyss/​2.0.2+$ sudo chown aorth /​export/​apps/​abyss/​2.1.4
 $ make install $ make install
-$ sudo chown -R root:root /​export/​apps/​abyss/​2.0.2</​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.txt · Last modified: 2019/07/10 17:25 by aorth