Thursday, 17 December 2009

ABySS: A parallel assembler for short read sequence data

new version available
reinstall in CentOS

sudo yum install openmpi

 ./configure --prefix=/opt/ABySS --with-mpi=/usr/lib/openmpi CPPFLAGS=-I/usr/include  && make

sudo make install

Trying to install this for de novo transcriptome assembly

checking how to run the C++ preprocessor... /lib/cpp
configure: error: in `/home/k/bin/source/abyss-1.0.16':
configure: error: C++ preprocessor "/lib/cpp" fails sanity check
See `config.log' for more details.

|              Syntax error
configure:6628: /lib/cpp   conftest.cpp
cpp: error trying to exec 'cc1plus': execvp: No such file or directory
configure:6628: $? = 1
configure: failed program was:
| /* confdefs.h */

Had the above error

then tried
  yum install gcc-c++
fingers crossed

Part 2 of install woes

well the above worked but i got this at the end of configure

warning: ABySS should be compiled with Google sparsehash to
        reduce memory usage. It may be downloaded here:

Hmmm you would think they would mention this in the 1st line of the README
two options I want
If you wish to build the parallel assembler with MPI support,
MPI should be found in /usr/include and /usr/lib or its location
specified to configure:
./configure --with-mpi=/usr/lib/openmpi && make

ABySS should be built using Google sparsehash to reduce memory usage,
although it will build without. Google sparsehash should be found in
/usr/include or its location specified to configure:
./configure CPPFLAGS=-I/usr/local/include

1 comment:

  1. Just incase anyone else has the same problem: I tried this suggestion and it didn't work BUT sudo apt-get install g++ did! Cheers.


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