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Korištenje
Dostupne verzije su:
Verzija | Modul |
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1.40.4 | mothur/1.40.4 |
1.48.0 | mothur/1.48.0 |
Mothur se koristi interaktivno stoga kad proslijeđujemo u obliku command line-a pišemo.
Code Block | ||||
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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()" |
Dokumentacija naredbi: https://mothur.org/wiki/tags/#file_types
Primjer je napisa u skladu sa podnošenjem posla na čvor prema https://mothur.org/wiki/miseq_sop/ primjeru analize.
Code Block | ||||
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#!/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)" |
Prije instalacije same aplikacije instalirane su potrebne knjižnice.
HDF5 je instaliran sa prevoditeljem intel/2020. Verzija knjižnice je sa cxx i fortran prevoditeljem prevedena.
Izvorni kod je skinut sa https://portal.hdfgroup.org/display/support/HDF5+1.13.0 .
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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 |
GLS je instaliran sa prevoditeljem intel/2020
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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 |
Boost knjižnica je bila već instalirana
Izmjene u Makefile-u:
Code Block | ||||
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OPTIMIZE ?= yes
USEREADLINE ?= no
USEBOOST ?= yes
USEHDF5 ?= yes
USEGSL ?= yes
LOGFILE_NAME ?= no
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
MOTHUR_FILES="\"Enter_your_default_path_here\""
MOTHUR_TOOLS="\"Enter_your_mothur_tools_path_here\""
VERSION = "\"1.48.0\""
RELEASE_DATE = "\"5/20/22\"" |
Instalacija je izvršena s prevoditeljem openmpi41-intel-x86_64
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module load mpi/openmpi41-intel-x86_64
export LD_LIBRARY_PATH=/apps/boost/1.70/avx2/lib:/apps/hdf5/1.13.0_fortran_cxx/lib:/apps/gsl/2.7.1/lib
cd mothur-1.48.0
make -j8 CC=mpicc CXX=mpicxx |