User Tools

Site Tools



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 [2015/03/16 06:38]
aorth [Abyss]
abyss-software [2019/07/10 14:25] (current)
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:   * Link:
 ===== 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 +wget 
-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 [[|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