https://www.mothur.org/

Korištenje

Dostupne verzije su:

VerzijaModul

1.40.4

mothur/1.40.4

1.48.0

mothur/1.48.0

Mothur je po prirodi interaktivan program, no postoji način i upisivanja direktno u terminal bez ulaženja u mothur-ovu konzolu.

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 dokumentacija naredbi je dostupna na https://mothur.org/wiki/tags/#file_types

Primjer je napisan u skladu s podnošenjem posla na čvor prema https://mothur.org/wiki/miseq_sop/ primjeru analize.

Primjer korištenja: mothur-teran.sge
#!/bin/bash

#$ -cwd
#$ -pe *mpisingle 16

# load program environment
module load mothur/1.48.0

# run the program
mothur "#make.contigs(file=stability.files, processors=$NSLOTS)"

Važno

Isključivo se koristiti sa *mpisingle 2-28 ili *mpifull 28.

Prije instalacije same aplikacije, instalirane su potrebne knjižnice.

HDF5 je instaliran s prevoditeljem intel/2020. Verzija knjižnice je s cxx i fortran prevoditeljima prevedena.

Izvorni kod je skinut s https://portal.hdfgroup.org/display/support/HDF5+1.13.0 .

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 s prevoditeljem intel/2020

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:

Makefile
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/
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 intel/2020

module load intel/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=icc CXX=icpc
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