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Config.txt
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# Contig.txt - part of RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets
# Copyright (C) 2009-2016 Ariane Belka, Maria Jenckel, Matthias Scheuch, Dirk Hoeper
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#!/bin/bash
#################################################################### Please adapt ########################################################################
##########################################################################################################################################################
########################################## Software paths
gsflxdir=path-name/454_3.0/bin/ # directory containg all GS FLX applications (e.g. sfffile, runAssembly etc.)
installdir=path-name/RIEMS/ # install directory containing all 'RIEMS' subtools (e.g. TrimSff.sh etc.)
embossdir=path-name/emboss/bin/ # directory containg all Emboss software applications (e.g. sixpack etc.)
blastdir=path-name/ncbi-blast-2.4.0+/bin/ # directory containg all BLAST software applications (e.g. blastn, makeblastdb etc.)
R=/usr/lib64/R/bin/ # path to R
latexdir=/usr/bin/ # path to Latex
########################################## Database paths
BLASTDB=path-name/ncbi/ # path to blastdbs
export BLASTDB # export path to blastdbs
ntdb=nt # BLAST nucleotide database
protdb=nr # BLAST non redundant database
taxdir=path-name/taxonomy # directory containing BLAST '.dmp' files (e.g. names.dmp, gi_taxid_nucl.dmp etc.)
fasttaxid=path-name/taxLok # directory containing viral database (automatically created after each BLAST db update)
fasttaxidntdb=$fasttaxid/gi_taxid_nucl/gi_taxid_nucl # database for fast nucl gi -> taxid assignment | (automatically created
fasttaxidprotdb=$fasttaxid/gi_taxid_prot/gi_taxid_prot # database for fast prot gi -> taxid assignment V after each BLAST db update)
refseqdir=$installdir/RefSequenzen # optional: directory containing downloaded references during analyses
########################################## Variables
threads=`grep -c ^processor /proc/cpuinfo` # number of CPU threads 'RIEMS' may use (the more, the faster!)
((threadsSplit=threads-1)) # number of files created during several steps within RIEMS
((threadsMap=threads/2-1))
((threadsMax=100)) # max number of files created in several steps within RIEMS (also restricted by suffixes/prefexes)
evalue=0.001 # E-value limit for all BLAST analyses
LC_NUMERIC=C
cutoffAssembly=250000 # cut-off unclassified reads for Assembley
cutoffRndReads=200000 # cut-off unclassified reads for blast of random reads
Rrespository=https://cran.uni-muenster.de/ # set respository for R-packages
export Rrespository # export respository for R-packages
########################################## Scripts
scriptR=${installdir}/resultprotocol.R # path to R script for result tables
scriptT=${installdir}/resultprotocol.Rnw # path to Rnw file for result report
scriptBlastp=${installdir}/Blastp.R # path to R script for Blastp results
scriptFurther=${installdir}/resultprotocol_further.R # path to R script for result tables
scriptTFurther=${installdir}/resultprotocol_further.Rnw # path to Rnw script for result report
########################################## Files
referenz_trimming=${installdir}/dummy.fna # path to dummy-reference
il_adapter=${installdir}/illuminaAdapterTrimmingDB.fna # path to illumina adapter sequences
it_adapter=${installdir}/dummy.fna # path to ion torrent adapter sequences