application.properties.example 13.3 KB
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#
# Copyright (C) 2015 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/>.
#
[global]
# uncomment and set if not in the PATH,  should be version >= 4.4.3
#makeflow = /usr/bin/makeflow
# batch system type: local, condor, sge, moab, cluster, wq, hadoop, mpi-queue
batch_system_type = local
# add these options to all batch submit files
batch_options = 
# add these options to limit the number of jobs sumitted in parallel
limit_submission = 100
# on which socket host should run the web server
server_socket_host = 127.0.0.1
# on which socket port should run the web server
server_socket_port = 8080
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#server_socket_port = 8083
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# protocol used to access web server (http|https)
server_socket_protocol = https
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# date format
date_format = %d/%m/%Y

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#optional : key for jflow server ssl configuration
ssl_certificate = certificate.crt
ssl_certificate_chain = certificate_chain.crt
ssl_private_key = private_key.key
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[email]
# if you want an email to be sent at the end of the workflow execution
# set the smtp_server and the from_address values
smtp_server = 
smtp_port = 
from_address = 
from_password = 
# uncomment and set if you want to use these values for all the workflow
# these variables can be overloaded within the workflow implementation by
# using self.set_to_address("address"), self.set_subject("subject"), 
# self.set_message("message") functions
#to_address =
#subject =
#message =
#Purge email configuration
#if you want to use purge option, an email is sent
#In purge email you can fix for an extention : 
# the minimal duration
min_extension_duration = 1 year
# the minimal size
min_extension_size = 1 Tbite
# the price for min_extension_duration * min_extension_size
min_extension_price = 300 Euros
# delay (in days) after sending an email to indicate that the data will be deleted  
delay_purge = 30
# the url where prices are defined
url_extension_price = http://url.extention.prices

[database]
host = localhost
user = typo3
passwd = typo3
dbname = typo3

[storage]
# where should be written the log file
log_file = <path>/ng6.log
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#level of logs to display in log_file
log_level = logging.DEBUG|logging.WARNING|logging.ERROR|...
# Where should data be stored
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save_directory = <path>/ng6
# Where should the pipelines write results, should be accessible 
# by all cluster nodes
work_directory = <path>/work
# Where should the pipelines write temporary files, should be 
# accessible by all cluster nodes
tmp_directory = <path>/tmp

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# Configure different storage directory 
# and associate retention date or duration
#
# eg with a duration
[space_default]
dir_name=default
retention_period=3
#
# eg with a fix date
[space_final]
dir_name=directory
retention_date=12/03/2021

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[ui]
# This must be an absolute path of a directory mounted and accessible by the server 
user_base_directory = /work/

# where could be find binaries
[softwares]
# uncomment and set if not in the PATH
#
# Global softwares
#
#cutadapt = /usr/bin/cutadapt
#blastall = /usr/bin/blastall
#formatdb = /usr/bin/formatdb
#blastn = /usr/bin/blastn
#blastx = /usr/bin/blastx
#makeblastdb = /usr/bin/makeblastdb
#bwa = /usr/bin/bwa
#samtools = /usr/bin/samtools
#ktImportBLAST = /usr/local/bin/ktImportBLAST
#fastqc = /nosave/software/fastqc/current/fastqc
#fastq_illumina_filter = /usr/bin/fastq_illumina_filter
#CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar
#MarkDuplicates = /usr/bin/MarkDuplicates.jar
#mothur = /usr/bin/mothur
#fastx_reverse_complement = /usr/bin/fastx_reverse_complement
#STAR = /usr/bin/STAR
#fastuniq = /usr/local/bin/fastuniq
#javaPICARD = /tools/java/jre1.8.0_45/bin/java
# workflow specific
#

# r454_qc
#sfffile = /usr/bin/sfffile
#runAssembly = /usr/bin/runAssembly

# illumina_rnaseq
#geneBody_coverage.py = /usr/local/bin/geneBody_coverage.py
#infer_experiment.py = /usr/local/bin/infer_experiment.py
#inner_distance.py = /usr/local/bin/inner_distance.py
#junction_saturation.py = /usr/local/bin/junction_saturation.py
#RPKM_saturation.py = /usr/local/bin/scripts/RPKM_saturation.py
#junction_annotation.py = /usr/local/bin/junction_annotation.py
#NormalizeFasta.jar = /usr/local/bin/NormalizeFasta.jar


# radseq
#ustacks = /usr/local/bin/ustacks
#cstacks = /usr/local/bin/cstacks

# methylseq
#trim_galore = /nosave/software/trim_galore
#bismark = /nosave/software/bismark_v0.8.3/bismark
#bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation
#bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor
#for rmdup samtools_old v 0.19
#samtools_old = /usr/bin/samtools

# gene_diversity
#framebot = /usr/bin/FrameBot.jar
#usearch = /usr/bin/usearch
#cdhit = /usr/bin/cd-hit
#ktImportText = /usr/local/bin/ImportText.pl

# pacbio_qc
#fofnToSmrtpipeInput.py = $INSTALLDI/current/analysis/bin/fofnToSmrtpipeInput.py
#smrtpipe = $INSTALLDIR/current/smrtcmds/bin/smrtpipe

# Set cluster parameters of some components
[components]
#Bismark.batch_options = -pe parallel_smp 8 -q wflowq
#BismarkMethylationExtractor.batch_options = -l mem=8G -l h_vmem=16G -q wflowq
#BWA.batch_options = -q unlimitq
#AlignmentStats.batch_options = -q unlimitq
#ContaminationSearch.batch_options = -q unlimitq
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#Trim_porechop.batch_options = --mem=4G -p wflowq -t 30
#Trim_porechop.modules = compiler/gcc-7.2.0,bioinfo/Porechop-0.2.1
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# Set workflows group
[workflows]
# download workflows
DownloadArchive.group = download
DownloadSymlink.group = download 
DownloadURL.group = download

# run workflows
AddRun.group = addrun 
GeneDiversity.group = addrun
IlluminaDiversityQC.group = addrun
IlluminaMatePair.group = addrun
IlluminaQualityCheck.group = addrun
RnaSeqQualityCheck.group = addrun
Methylseq.group = addrun
PacBioQualityCheck.group = addrun
PhiXCheck.group = addrun
R454QualityCheck.group = addrun

[resources]
typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip
#phix_bwa = /bank/bwadb/phi.fa
#ecoli_bwa = /bank/bwadb/ecoli536
#yeast_bwa = /bank/bwadb/yeast.nt

[454_mids]
MID1 = ACGAGTGCGT
MID2 = ACGCTCGACA
MID3 = AGACGCACTC
MID4 = AGCACTGTAG
MID5 = ATCAGACACG
MID6 = ATATCGCGAG
MID7 = CGTGTCTCTA
MID8 = CTCGCGTGTC
MID9 = TAGTATCAGC
MID10 = TCTCTATGCG
MID11 = TGATACGTCT
MID12 = TACTGAGCTA
MID13 = CATAGTAGTG
MID14 = CGAGAGATAC
MID15 = ATACGACGTA
MID16 = TCACGTACTA
MID17 = CGTCTAGTAC
MID18 = TCTACGTAGC
MID19 = TGTACTACTC
MID20 = ACGACTACAG
MID21 = CGTAGACTAG
MID22 = TACGAGTATG
MID23 = TACTCTCGTG
MID24 = TAGAGACGAG
MID25 = TCGTCGCTCG
MID26 = ACATACGCGT
MID27 = ACGCGAGTAT
MID28 = ACTACTATGT
MID29 = ACTGTACAGT
MID30 = AGACTATACT
MID31 = AGCGTCGTCT
MID32 = AGTACGCTAT
MID33 = ATAGAGTACT
MID34 = CACGCTACGT
MID35 = CAGTAGACGT
MID36 = CGACGTGACT
MID37 = TACACACACT
MID38 = TACACGTGAT
MID39 = TACAGATCGT
MID40 = TACGCTGTCT
MID41 = TAGTGTAGAT
MID42 = TCGATCACGT
MID43 = TCGCACTAGT
MID44 = TCTAGCGACT
MID45 = TCTATACTAT
MID46 = TGACGTATGT
MID47 = TGTGAGTAGT
MID48 = ACAGTATATA
MID49 = ACGCGATCGA
MID50 = ACTAGCAGTA
MID51 = AGCTCACGTA
MID52 = AGTATACATA
MID53 = AGTCGAGAGA
MID54 = AGTGCTACGA
MID55 = CGATCGTATA
MID56 = CGCAGTACGA
MID57 = CGCGTATACA
MID58 = CGTACAGTCA
MID59 = CGTACTCAGA
MID60 = CTACGCTCTA
MID61 = CTATAGCGTA
MID62 = TACGTCATCA
MID63 = TAGTCGCATA
MID64 = TATATATACA
MID65 = TATGCTAGTA
MID66 = TCACGCGAGA
MID67 = TCGATAGTGA
MID68 = TCGCTGCGTA
MID69 = TCTGACGTCA
MID70 = TGAGTCAGTA
MID71 = TGTAGTGTGA
MID72 = TGTCACACGA
MID73 = TGTCGTCGCA
MID74 = ACACATACGC
MID75 = ACAGTCGTGC
MID76 = ACATGACGAC
MID77 = ACGACAGCTC
MID78 = ACGTCTCATC
MID79 = ACTCATCTAC
MID80 = ACTCGCGCAC
MID81 = AGAGCGTCAC
MID82 = AGCGACTAGC
MID83 = AGTAGTGATC
MID84 = AGTGACACAC
MID85 = AGTGTATGTC
MID86 = ATAGATAGAC
MID87 = ATATAGTCGC
MID88 = ATCTACTGAC
MID89 = CACGTAGATC
MID90 = CACGTGTCGC
MID91 = CATACTCTAC
MID92 = CGACACTATC
MID93 = CGAGACGCGC
MID94 = CGTATGCGAC
MID95 = CGTCGATCTC
MID96 = CTACGACTGC
MID97 = CTAGTCACTC
MID98 = CTCTACGCTC
MID99 = CTGTACATAC
MID100 = TAGACTGCAC
MID101 = TAGCGCGCGC
MID102 = TAGCTCTATC
MID103 = TATAGACATC
MID104 = TATGATACGC
MID105 = TCACTCATAC
MID106 = TCATCGAGTC
MID107 = TCGAGCTCTC
MID108 = TCGCAGACAC
MID109 = TCTGTCTCGC
MID110 = TGAGTGACGC
MID111 = TGATGTGTAC
MID112 = TGCTATAGAC
MID113 = TGCTCGCTAC
MID114 = ACGTGCAGCG
MID115 = ACTCACAGAG
MID116 = AGACTCAGCG
MID117 = AGAGAGTGTG
MID118 = AGCTATCGCG
MID119 = AGTCTGACTG
MID120 = AGTGAGCTCG
MID121 = ATAGCTCTCG
MID122 = ATCACGTGCG
MID123 = ATCGTAGCAG
MID124 = ATCGTCTGTG
MID125 = ATGTACGATG
MID126 = ATGTGTCTAG
MID127 = CACACGATAG
MID128 = CACTCGCACG
MID129 = CAGACGTCTG
MID130 = CAGTACTGCG
MID131 = CGACAGCGAG
MID132 = CGATCTGTCG
MID133 = CGCGTGCTAG
MID134 = CGCTCGAGTG
MID135 = CGTGATGACG
MID136 = CTATGTACAG
MID137 = CTCGATATAG
MID138 = CTCGCACGCG
MID139 = CTGCGTCACG
MID140 = CTGTGCGTCG
MID141 = TAGCATACTG
MID142 = TATACATGTG
MID143 = TATCACTCAG
MID144 = TATCTGATAG
MID145 = TCGTGACATG
MID146 = TCTGATCGAG
MID147 = TGACATCTCG
MID148 = TGAGCTAGAG
MID149 = TGATAGAGCG
MID150 = TGCGTGTGCG
MID151 = TGCTAGTCAG
MID152 = TGTATCACAG
MID153 = TGTGCGCGTG
RL1 = ACACGACGACT,AGTCGTGGTGT
RL2 = ACACGTAGTAT,ATACTAGGTGT
RL3 = ACACTACTCGT,ACGAGTGGTGT
RL4 = ACGACACGTAT,ATACGTGGCGT
RL5 = ACGAGTAGACT,AGTCTACGCGT
RL6 = ACGCGTCTAGT,ACTAGAGGCGT
RL7 = ACGTACACACT,AGTGTGTGCGT
RL8 = ACGTACTGTGT,ACACAGTGCGT
RL9 = ACGTAGATCGT,ACGATCTGCGT
RL10 = ACTACGTCTCT,AGAGACGGAGT
RL11 = ACTATACGAGT,ACTCGTAGAGT
RL12 = ACTCGCGTCGT,ACGACGGGAGT
RL13 = AGACTCGACGT,ACGTCGGGTCT
RL14 = AGTACGAGAGT,ACTCTCGGACT
RL15 = AGTACTACTAT,ATAGTAGGACT
RL16 = AGTAGACGTCT,AGACGTCGACT
RL17 = AGTCGTACACT,AGTGTAGGACT
RL18 = AGTGTAGTAGT,ACTACTAGACT
RL19 = ATAGTATACGT,ACGTATAGTAT
RL20 = CAGTACGTACT,AGTACGTGCTG
RL21 = CGACGACGCGT,ACGCGTGGTCG
RL22 = CGACGAGTACT,AGTACTGGTCG
RL23 = CGATACTACGT,ACGTAGTGTCG
RL24 = CGTACGTCGAT,ATCGACGGACG
RL25 = CTACTCGTAGT,ACTACGGGTAG
RL26 = GTACAGTACGT,ACGTACGGTAC
RL27 = GTCGTACGTAT,ATACGTAGGAC
RL28 = GTGTACGACGT,ACGTCGTGCAC
RL29 = ACACAGTGAGT,ACTCACGGTGT
RL30 = ACACTCATACT,AGTATGGGTGT
RL31 = ACAGACAGCGT,ACGCTGTGTGT
RL32 = ACAGACTATAT,ATATAGTGTGT
RL33 = ACAGAGACTCT,AGAGTCTGTGT
RL34 = ACAGCTCGTGT,ACACGAGGTGT
RL35 = ACAGTGTCGAT,ATCGACAGTGT
RL36 = ACGAGCGCGCT,AGCGCGCGCGT
RL37 = ACGATGAGTGT,ACACTCAGCGT
RL38 = ACGCGAGAGAT,ATCTCTGGCGT
RL39 = ACGCTCTCTCT,AGAGAGGGCGT
RL40 = ACGTCGCTGAT,ATCAGCGGCGT
RL41 = ACGTCTAGCAT,ATGCTAGGCGT
RL42 = ACTAGTGATAT,ATATCACGAGT
RL43 = ACTCACACTGT,ACAGTGGGAGT
RL44 = ACTCACTAGCT,AGCTAGGGAGT
RL45 = ACTCTATATAT,ATATATGGAGT
RL46 = ACTGATCTCGT,ACGAGATGAGT
RL47 = ACTGCTGTACT,AGTACAGGAGT
RL48 = ACTGTAGCGCT,AGCGCTAGAGT
RL49 = AGACACTCACT,AGTGAGGGTCT
RL50 = AGACATATAGT,ACTATAGGTCT
RL51 = AGACGTGATCT,AGATCAGGTCT
RL52 = AGAGTACAGAT,ATCTGTAGTCT
RL53 = AGAGTATCTCT,AGAGATAGTCT
RL54 = AGATACGCTGT,ACAGCGTGTCT
RL55 = AGATCTAGTCT,AGACTAGGTCT
RL56 = AGCAGCGTAGT,ACTACGCGGCT
RL57 = AGCGCACGAGT,ACTCGTGGGCT
RL58 = AGCGTGTGCGT,ACGCACAGGCT
RL59 = AGCTAGATACT,AGTATCTGGCT
RL60 = AGCTGTCGACT,AGTCGACGGCT
RL61 = AGTATGCACGT,ACGTGCAGACT
RL62 = AGTCGCGCTAT,ATAGCGGGACT
RL63 = AGTCTGTCTGT,ACAGACGGACT
RL64 = ATACACACGAT,ATCGTGGGTAT
RL65 = ATACGCGTGCT,AGCACGGGTAT
RL66 = ATACTAGCACT,AGTGCTGGTAT
RL67 = ATAGAGCTAGT,ACTAGCTGTAT
RL68 = ATATAGAGTAT,ATACTCTGTAT
RL69 = ATCGCTCACGT,ACGTGAGGGAT
RL70 = ATCGTCAGTCT,AGACTGAGGAT
RL71 = ATCTCTCGTAT,ATACGAGGGAT
RL72 = ATCTGAGACGT,ACGTCTCGGAT
RL73 = ATGCTACGTCT,AGACGTGGCAT
RL74 = ATGTGACTACT,AGTAGTCGCAT
RL75 = CACGAGACAGT,ACTGTCTGGTG
RL76 = CACGCGAGTCT,AGACTCGGGTG
RL77 = CACGCTACGAT,ATCGTAGGGTG
RL78 = CACGTGTATAT,ATATACAGGTG
RL79 = CACTACGATGT,ACATCGTGGTG
RL80 = CACTATACTCT,AGAGTATGGTG
RL81 = CAGCGTACTGT,ACAGTAGGCTG
RL82 = CAGTCTCTAGT,ACTAGAGGCTG
RL83 = CATAGTCGCGT,ACGCGACGATG
RL84 = CGAGACACTAT,ATAGTGTGTCG
RL85 = CGAGAGTGTGT,ACACACTGTCG
RL86 = CGAGTCATCGT,ACGATGAGTCG
RL87 = CGATCGTATAT,ATATACGGTCG
RL88 = CGCAGTACGCT,AGCGTACGGCG
RL89 = CGCGATCGTAT,ATACGATGGCG
RL90 = CGCGCTATACT,AGTATAGGGCG
RL91 = CGTACAGATAT,ATATCTGGACG
RL92 = CGTAGCTCTCT,AGAGAGCGACG
RL93 = CGTATAGTGCT,AGCACTAGACG
RL94 = CGTCAGCGACT,AGTCGCGGACG
RL95 = CGTCGCAGTGT,ACACTGGGACG
RL96 = CGTCTCACGAT,ATCGTGGGACG
RL97 = CGTGACTCAGT,ACTGAGTGACG
RL98 = CTACACGCTCT,AGAGCGGGTAG
RL99 = CTACGATATGT,ACATATGGTAG
RL100 = CTAGACAGACT,AGTCTGTGTAG
RL101 = CTAGTACTCAT,ATGAGTAGTAG
RL102 = CTATATGTCGT,ACGACATGTAG
RL103 = CTATCGACACT,AGTGTCGGTAG
RL104 = CTATGTAGAGT,ACTCTACGTAG
RL105 = CTCACGTACAT,ATGTACGGGAG
RL106 = CTCGAGTCTCT,AGAGACTGGAG
RL107 = CTCGTCGAGAT,ATCTCGAGGAG
RL108 = CTCTACAGCGT,ACGCTGTGGAG
RL109 = CTGTCGTGCGT,ACGCACGGCAG
RL110 = CTGTGACGTGT,ACACGTCGCAG
RL111 = GACGCTGTCGT,ACGACAGGGTC
RL112 = GACGTATGACT,AGTCATAGGTC
RL113 = GACTAGCTAGT,ACTAGCTGGTC
RL114 = GAGACGTCGCT,AGCGACGGCTC
RL115 = GAGAGAGACGT,ACGTCTCGCTC
RL116 = GCGTAGACTAT,ATAGTCTGCGC
RL117 = GCGTCGTGTCT,AGACACGGCGC
RL118 = GCTCTCTACGT,ACGTAGGGAGC
RL119 = GTACACTGTAT,ATACAGGGTAC
RL120 = GTACGCGACAT,ATGTCGGGTAC
RL121 = GTACTATAGAT,ATCTATGGTAC
RL122 = GTACTGAGTCT,AGACTCGGTAC
RL123 = GTAGCTAGCGT,ACGCTAGGTAC
RL124 = GTAGTCACTGT,ACAGTGAGTAC
RL125 = GTAGTGTCACT,AGTGACAGTAC
RL126 = GTATACATAGT,ACTATGTGTAC
RL127 = GTCATCGTCGT,ACGACGAGGAC
RL128 = GTCGACACGCT,AGCGTGTGGAC
RL129 = GTCGAGTGAGT,ACTCACTGGAC
RL130 = GTCTACTATCT,AGATAGTGGAC
RL131 = GTGTCTAGACT,AGTCTAGGCAC
RL132 = GTGTGTATCGT,ACGATACGCAC