I download SortMeRNA from http://bioinfo.lifl.fr/RNA/sortmerna/. However, when I do
I got error:
src/paralleltraversal.cpp:18:10: fatal error: 'omp.h' file not found #include
^ 1 error generated.
Then I tried to use a different gcc.
sudo port selfupdate sudo port install gcc48 sudo port install openmpi
After that Do:
./configure CC=/opt/local/bin/gcc-mp-4.8 CXX=g++-mp-4.8 make sudo make install
And I got:
qiuworld$ which sortmerna /usr/local/bin/sortmerna qiuworld$ sortmerna --version SortMeRNA version 1.9, 30/08/2013 30/08/2013 - fixed bug for naming output log file - modified merge-paired-reads.sh to work on a cluster 13/05/2013 - fixed bug to detect last (rRNA) read in fastq file - modified merge/unmerge-paired-reads.sh 05/04/2013 - changed to the usual 'configure, make, make install' (see the user manual v1.7) - added 'merge-paired-reads.sh' and 'unmerge-paired-reads.sh' for forward-reverse paired-end reads (see the user manual v1.7) - fixed an integer overflow for mmap calculation for 32-bit 26/02/2013 - changed sysconf library to sysctl for Mac OS - the sequence tag in the provided rRNA databases now follows the format: >[accession] [taxonomy] [length] 15/02/2013 - error for output of paired reads >1GB resolved - option -m added for specifying the amount of memory for loading reads - reads of length < L (default L=18) are automatically considered as non-rRNA - local timestamp added to --log statistics file 06/02/2013 - reads up to 5000 nucleotides supported (Illumina or 454 technology) - AUTHORS file added to SortMeRNA directory 24/01/2013 - L=20 error messages resolved - I/O file checks modified - Makefile updated for setting $SORTMERNADIR - support for paired-end reads 04/01/2013 - input directory can be current without any path 20/12/2012 - reads input files without an extension allowed