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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 pišemoje po prirodi interaktivan program, no postoji način i upisivanja direktno u terminal bez ulaženja u mothur-ovu konzolu.
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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: Potpuna 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.
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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$NSLOTS)" |
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Isključivo se koristiti sa *mpisingle 2-28 ili *mpifull 28. |
Prije instalacije same aplikacije, instalirane su potrebne knjižnice.
HDF5 je instaliran sa s prevoditeljem intel/2020. Verzija knjižnice je sa s cxx i fortran prevoditeljem prevoditeljima prevedena.
Izvorni kod je skinut sa s https://portal.hdfgroup.org/display/support/HDF5+1.13.0 .
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module load intel/2020 CC=icc CXX=icpc FC=ifort F90=ifort ./configure --prefix=/home/mhrzenja/mothur/hdf5/hdf5 --enable-fortran --enable-cxx make make install |
GLS GSL je instaliran sa s prevoditeljem intel/2020
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module load intel/2020 wget https://mirror.easyname.at/gnu/gsl/gsl-latest.tar.gz tar -xvzf gsl-latest.tar.gz cd gsl-latest ./configure CC=icc CXX=icpc --prefix=/home/mhrzenja/mothur/gsl-comp make && make install |
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OPTIMIZE ?= yes USEREADLINE ?= no USEBOOST ?= yes USEHDF5 ?= yes USEGSL ?= yes LOGFILE_NAME ?= no BOOST_LIBRARY_DIR ?= /apps/boost/1.70/avx2/lib BOOST_INCLUDE_DIR ?= /apps/boost/1.70/avx2/include/boost HDF5_LIBRARY_DIR ?= /apps/hdf5/1.13.0_fortran_cxx/lib HDF5_INCLUDE_DIR ?= /apps/hdf5/1.13.0_fortran_cxx/include GSL_LIBRARY_DIR ?= /apps/gsl/2.7.1/lib GSL_INCLUDE_DIR ?= /apps/gsl/2.7.1/include MOTHUR_FILES="\"Enter_your_default_path_here\"" MOTHUR_TOOLS="\"Enter_your_mothur_tools_path_here\"" VERSION = "\"1.48.0\"" RELEASE_DATE = "\"5/20/22\"" |
Instalacija je izvršena s prevoditeljem openmpi41-intel-x86_64intel/2020
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module load mpi/openmpi41-intel-x86_64intel/2020 export LD_LIBRARY_PATH=/apps/boost/1.70/avx2/lib:/apps/hdf5/1.13.0_fortran_cxx/lib:/apps/gsl/2.7.1/lib:$LD_LIBRARY_PATH cd mothur-1.48.0 make -j8 CC=mpiccicc CXX=mpicxxicpc |