User Tools

Site Tools


abyss-software

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
abyss-software [2014/08/28 13:11]
aorth
abyss-software [2019/07/10 17:25] (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: 1.5.2+  * 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'​s ​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'​s ​OpenMPI]] so we have to set the environment variables manually before building.
abyss-software.1409220716.txt.gz · Last modified: 2014/08/28 13:11 by aorth