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config.sh
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#
# Copyright (C) 2016 INRA
#
# 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/>.
#
#----------------------------------------------------------------------
#authors :
#---------
# Piumi Francois ([email protected]) software conception and development (engineer in bioinformatics)
# Jouneau Luc ([email protected]) software conception and development (engineer in bioinformatics)
# Gasselin Maxime ([email protected]) software user and data analysis (PhD student in Epigenetics)
# Perrier Jean-Philippe ([email protected]) software user and data analysis (PhD student in Epigenetics)
# Al Adhami Hala ([email protected]) software user and data analysis (postdoctoral researcher in Epigenetics)
# Jammes Helene ([email protected]) software user and data analysis (research group leader in Epigenetics)
# Kiefer Helene ([email protected]) software user and data analysis (principal invertigator in Epigenetics)
#
#Path to the directory where RRBS pipeline is installed (directory where this configuration file is located)
RRBS_HOME=/save/bdr-er5/RRBS-toolkit
#path to the directory where bismark is installed
BISMARK_HOME=/usr/local/bioinfo/src/Bismark/bismark_v0.14.3
#path to the directory where bowtie (v1) is installed
BOWTIE_HOME=/usr/local/bioinfo/src/bowtie/bowtie-0.12.9
#path to the trim_galore executable file
TRIMGALORE_EXECUTE=/usr/local/bioinfo/src/Trim_Galore/trim_galore_v0.4.0/trim_galore
#path to the cut_adapt executable file
#CUTADAPT_EXECUTE=/usr/local/bioinfo/src/cutadapt/cutadapt-1.7.1/bin/cutadapt
CUTADAPT_EXECUTE=/usr/local/bioinfo/src/python/current/bin/cutadapt
#path to the samtools executable file
SAMTOOLS_EXECUTE=/usr/local/bioinfo/src/samtools/samtools-1.1/samtools
#path to the python (v2.7) executable file
PYTHON_EXECUTE=/usr/local/bioinfo/src/python/Python-2.7.2/bin/python
#path to the R executable file
R_EXECUTE=/usr/local/bioinfo/bin/R
export RRBS_HOME BISMARK_PIPELINE_HOME BISMARK_HOME BOWTIE_HOME TRIMGALORE_EXECUTE CUTADAPT_EXECUTE SAMTOOLS_EXECUTE PYTHON_EXECUTE R_EXECUTE