...
| Code Block |
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| language | bash |
|---|
| title | Command line primjer |
|---|
|
mothur "#dist.seqs(fasta=final.fasta, processors=12)"
#lančanje naredbi
mothur "#dist.seqs(fasta=final.fasta, processors=12);cluster(column=current, count=final.count_table);collect.single();rarefaction.single()" |
Potpuna okumentacija dokumentacija naredbi je dostupna na https://mothur.org/wiki/tags/#file_types
Primjer je napisa napisan u skladu sa s podnošenjem posla na čvor prema https://mothur.org/wiki/miseq_sop/ primjeru analize.
| Code Block |
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| language | bash |
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| title | Primjer korištenja: mothur-teran.sge |
|---|
|
#!/bin/bash
#$ -cwd
#$ -pe p28-*mpisingle 16
# load program environment
module load mothur/1.48.0
# run the program
mothur "#make.contigs(file=stability.files, processors=16$NSLOTS)" |
| Warning |
|---|
|
Isključivo se koristiti sa *mpisingle 2-28 ili *mpifull 28. |
Prije instalacije same aplikacije, instalirane su potrebne knjižnice.
HDF5 je instaliran sa s prevoditeljem intel/2020. Verzija knjižnice je sa s cxx i fortran prevoditeljem prevoditeljima prevedena.
Izvorni kod je skinut sa s https://portal.hdfgroup.org/display/support/HDF5+1.13.0 .
| Code Block |
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module load intel/2020
CC=icc CXX=icpc FC=ifort F90=ifort ./configure --prefix=/home/mhrzenja/mothur/hdf5/hdf5 --enable-fortran --enable-cxx
make
make install |
GSL je instaliran sa s prevoditeljem intel/2020
| Code Block |
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module load intel/2020
wget https://mirror.easyname.at/gnu/gsl/gsl-latest.tar.gz
tar -xvzf gsl-latest.tar.gz
cd gsl-latest
./configure CC=icc CXX=icpc --prefix=/home/mhrzenja/mothur/gsl-comp
make && make install |
...
| Code Block |
|---|
| language | bash |
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| title | Makefile |
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|
USEREADLINE ?= no
USEBOOST ?= yes
USEHDF5 ?= yes
USEGSL ?= yes
BOOST_LIBRARY_DIR ?= /apps/boost/1.70/avx2/lib
BOOST_INCLUDE_DIR ?= /apps/boost/1.70/avx2/include/boost
HDF5_LIBRARY_DIR ?= /apps/hdf5/1.13.0_fortran_cxx/lib
HDF5_INCLUDE_DIR ?= /apps/hdf5/1.13.0_fortran_cxx/include
GSL_LIBRARY_DIR ?= /apps/gsl/2.7.1/lib
GSL_INCLUDE_DIR ?= /apps/gsl/2.7.1/include
|
...
Instalacija je izvršena s prevoditeljem openmpi41-intel-x86_64intel/2020
| Code Block |
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module load mpi/openmpi41-intel-x86_64intel/2020
export LD_LIBRARY_PATH=/apps/boost/1.70/avx2/lib:/apps/hdf5/1.13.0_fortran_cxx/lib:/apps/gsl/2.7.1/lib:$LD_LIBRARY_PATH
cd mothur-1.48.0
make -j8 CC=mpiccicc CXX=mpicxxicpc |