-
Notifications
You must be signed in to change notification settings - Fork 19
/
settings_nightly.ini
133 lines (119 loc) · 6.35 KB
/
settings_nightly.ini
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
;This configuration file sets paths to tools, databases, etc.
;[path] is replaced by the base directory path of the GIT repository, i.e. it allows using relative paths.
;
;If you use the download shell scripts in data/ to install tools, genomes and databases,
;only adapting the NGSD database credentials is necessary.
[tools-ngs]
python3 = /mnt/storage2/megSAP/tools/Python-3.10.9_2024.08.21/bin/python3.10
python27 = /mnt/storage2/megSAP/tools/Python-2.7.18/bin/python2.7
ngs-bits = /mnt/storage2/megSAP/tools/ngs-bits-2024_08-22-gfaa0bfa9/
samtools = /mnt/storage2/megSAP/tools/samtools-1.20/samtools
freebayes = /mnt/storage2/megSAP/tools/freebayes-1.3.6/freebayes
vcflib = /mnt/storage2/megSAP/tools/vcflib-1.0.3/build/
abra2 = java -Xmx16G -jar /mnt/storage2/megSAP/tools/abra2-2.23/abra2.jar
samblaster = /mnt/storage2/megSAP/tools/samblaster-0.1.26/samblaster
bwa = /mnt/storage2/megSAP/tools/bwa-0.7.18/bwa
bwa-mem2 = /mnt/storage2/megSAP/tools/bwa-mem2-2.2.1_x64-linux/bwa-mem2
bwa-mem2.SRV010 = /mnt/storage2/megSAP/tools/bwa-mem2-2.2.1_x64-linux/bwa-mem2.avx2
vep = /mnt/storage2/megSAP/tools/ensembl-vep-release-112.0/vep
vep_data = /mnt/storage2/megSAP/data/dbs/ensembl-vep-112/
perl_cpan = /mnt/storage2/megSAP/tools/perl_cpan/
interop = /mnt/storage2/megSAP/tools/interop-1.2.4-Linux-GNU/bin/summary
rscript = /mnt/storage2/megSAP/tools/R-4.1.0/bin/Rscript
clincnv = /mnt/storage2/megSAP/tools/ClinCNV-1.18.3/clinCNV.R
clincnv_cohorts = /mnt/storage2/megSAP/data/ClinCNV-cohorts/
circos = /mnt/storage2/megSAP/tools/circos-0.69-9/bin/circos
expansion_hunter = /mnt/storage2/megSAP/tools/ExpansionHunter-v5.0.0-linux_x86_64/bin/ExpansionHunter
splice_env = /mnt/storage2/megSAP/tools/SplicingTools/splice_env3_10/
REViewer = /mnt/storage2/megSAP/tools/REViewer-v0.2.7/REViewer-v0.2.7
happy = /mnt/storage2/megSAP/tools/hap.py-0.3.14/bin/hap.py
gatk = java -Xmx4G -jar /mnt/storage2/megSAP/tools/gatk-4.6.0.0/gatk-package-4.6.0.0-local.jar
orad = /mnt/storage2/megSAP/tools/orad_2_6_1/orad
[tools-longread]
minimap2 = /mnt/storage2/megSAP/tools/minimap2-2.28_x64-linux/minimap2
clair3 = /mnt/storage2/megSAP/tools/Clair3-v1.0.10/run_clair3.sh
clair3_models = /mnt/storage2/megSAP/tools/Clair3-v1.0.10/models
longphase = /mnt/storage2/megSAP/tools/longphase_v1.7.3/longphase_linux-x64
whatshap = /mnt/storage2/megSAP/tools/Python-3.10.9_19.08.24/bin/whatshap
pypy3 = /mnt/storage2/megSAP/tools/pypy3.9-v7.3.16-linux64/bin/pypy3
parallel = /mnt/storage2/megSAP/tools/parallel-20240722/bin/parallel
sniffles = /mnt/storage2/megSAP/tools/Python-3.10.9_19.08.24/bin/sniffles
straglr = /mnt/storage2/megSAP/tools/straglr-1.5.1/straglr.py
trf = /mnt/storage2/megSAP/tools/TRF_4.09/trf409.linux64
blastn = /mnt/storage2/megSAP/tools/ncbi-blast-2.16.0+/bin/blastn
modkit = /mnt/storage2/megSAP/tools/modkit_v0.3.2/modkit
straglrOn = /mnt/storage2/megSAP/tools/StraglrOn_v0.2.2/src/straglron.py
[tools-ngs-somatic]
strelka2 = /mnt/storage2/megSAP/tools/strelka-2.9.10.centos6_x86_64/bin/
varscan2 = java -jar /mnt/storage2/megSAP/tools/VarScan.v2.4.6/VarScan.v2.4.6.jar
manta = /mnt/storage2/megSAP/tools/manta-1.6.0.centos6_x86_64/bin/
msisensor = /mnt/storage2/megSAP/tools/msisensor-pro-1.2.0/msisensor-pro
mipgen = /mnt/storage2/megSAP/tools/MIPGEN/mipgen
umiVar2 = /mnt/storage2/megSAP/tools/umiVar2_2024_07/
hla_genotyper = /mnt/storage2/megSAP/tools/hla-genotyper-2022_05/genotyper.py
scarHRD = /mnt/storage2/megSAP/tools/scarHRD/R/cli_scarHRD.R
[tools-ngs-rna]
STAR = /mnt/storage2/megSAP/tools/STAR-2.7.11b/bin/Linux_x86_64_static/STAR
feature_counts = /mnt/storage2/megSAP/tools/subread-2.0.6/bin/featureCounts
arriba = /mnt/storage2/megSAP/tools/arriba_v2.4.0
umi_tools = /mnt/storage2/megSAP/tools/Python-3.10.9_2024.08.21/bin/umi_tools
kraken2 = /mnt/storage2/megSAP/tools/kraken2-2.1.3/bin/kraken2
[tools-primer]
tracetuner = /mnt/storage2/megSAP/tools/tracetuner_3.0.6beta/rel/Linux_64/ttuner
primer3 = /mnt/storage2/megSAP/tools/primer3-2.3.6/src/
GRCh37_data_folder = /mnt/storage2/megSAP/data_hg19/
[singularity-container]
container_folder = /mnt/storage2/megSAP/tools/singularity_container/
container_clair3-trio = v0.7
[folders]
local_data = /var/lib/mysql/misc/local_ngs_data_GRCh38/
data_folder = /mnt/storage2/megSAP/data/
test_data_folder = /mnt/storage2/megSAP/test_data/
project_folder['diagnostic'] = /mnt/storage2/projects/diagnostic/
project_folder['research'] = /mnt/storage1/projects/research/
project_folder['test'] = /mnt/storage3/projects/test/
project_folder['external'] = /mnt/storage3/projects/external/
[general]
copy_dbs_to_local_data = true
delete_fastq_files = false
cnv_bin_size_wgs = 1000
cnv_bin_size_shallow_wgs = 5000
cnv_bin_size_longread_wgs = 10000
use_bwa1 = false
file_access_group = f_ad_bi_l_medgen_access_storages
annotate_refseq_consequences = false
custom_columns_test['ngsd_counts'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;COUNTS;NGSD counts"
custom_columns_test['ngsd_nervous_system'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;GSC08;NGSD nervous system counts"
[dragen]
; transfer folder
dragen_in = /mnt/storage2/megSAP/dragen/in/
dragen_out = /mnt/storage2/megSAP/dragen/out/
; working/genome directory on the DRAGEN server
dragen_data = /staging/data/
dragen_genomes = /staging/genomes/
;sge settings
dragen_log = /mnt/storage2/megSAP/dragen/sge_log/
queues_dragen = "dragen_srv016"
;use SV calling files from dragen/NovaSeq X
use_dragen_sv_calling = false
[mysql-databases]
db_host['NGSD'] = ""
db_name['NGSD'] = ""
db_user['NGSD'] = ""
db_pass['NGSD'] = ""
db_host['NGSD_TEST'] = "sql.img.med.uni-tuebingen.de"
db_name['NGSD_TEST'] = "NGSD_nightly"
db_user['NGSD_TEST'] = "ngsd_nightly"
db_pass['NGSD_TEST'] = "wacRY5MfpXPQQx9M"
db_host['Probeneingang'] = ""
db_name['Probeneingang'] = ""
db_user['Probeneingang'] = ""
db_pass['Probeneingang'] = ""
[grid_engine]
queues_default = "default_srv010,default_srv011,default_srv012,default_srv013,default_srv014,default_srv015,default_srv020,default_srv023"
queues_research = "research_srv011,research_srv023"
queues_high_priority = "default_srv010,default_srv011,default_srv012,default_srv013,default_srv014,default_srv015,priority_srv010,priority_srv011,priority_srv012,priority_srv013,priority_srv014,priority_srv015,priority_srv020"
queues_high_mem = "highmem_srv010,highmem_srv011,highmem_srv012,highmem_srv013,highmem_srv014,highmem_srv015,highmem_srv020,highmem_srv023"
[mibi-server]
mibi_target = ""
mibi_key = ""