forked from jrflab/modules
-
Notifications
You must be signed in to change notification settings - Fork 1
/
config.inc
152 lines (123 loc) · 4.75 KB
/
config.inc
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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
ifndef CONFIG_INC
REF ?= b37
SEQ_PLATFORM ?= illumina
SAMPLE_SET_FILE ?= sample_sets.txt
SAMPLE_FILE ?= samples.txt
SAMPLE_SPLIT_FILE ?= samples.split.txt # generate using scripts/prepareFastq.sh [remove underscores from sample names]
##Interpreters
ANACONDA_PYTHON ?= python
PYTHON ?= python
PERL ?= perl
R ?= R
MY_RSCRIPT ?= Rscript
RSCRIPT ?= Rscript
# General python 2.7 environment
ANACONDA_27_ENV ?= $(HOME)/share/usr/anaconda-envs/anaconda-2.7
# SUFAM python environment
SUFAM_ENV ?= $(HOME)/share/usr/anaconda-envs/sufam-dev
MUTSIG_REPORT_ENV = $(HOME)/share/usr/anaconda-envs/mutsig-report-0.0.1
JARDIR ?= $(HOME)/share/usr/lib/java
# jrflab modules environment
JRFLAB_MODULES_ENV ?= $(HOME)/share/usr/anaconda-envs/jrflab-modules-0.1.4
### Applications
UNZIP ?= /usr/bin/unzip
FASTQC ?= $(PERL) $(HOME)/share/usr/FastQC/fastqc
MUTECT_JAR ?= $(JARDIR)/muTect-1.1.7.jar
BOWTIE ?= $(PERL) $(HOME)/share/usr/bowtie2-2.2.4/bowtie2
BWA ?= bwa
#PBWA ?= mpiexec $(HOME)/share/usr/bin/pBWA
#GSNAP ?= $(HOME)/share/usr/bin/gsnap
#GSNAP_REF ?= $(HOME)/share/references/gmapdb/
#GSNAP_MAPS ?= $(GSNAP_REF)/$(REF)/$(REF).maps
SAMTOOLS ?= samtools
SAMTOOLS2 ?= samtools
VCFUTILS ?= $(HOME)/share/usr/bin/vcfutils.pl
BCFTOOLS2 ?= bcftools
BCFTOOLS ?= bcftools
BEDTOOLS ?= $(HOME)/share/usr/bin/bedtools
BGZIP ?= $(HOME)/share/usr/bin/bgzip
IGVTOOLS ?= $(HOME)/share/usr/IGVTools/igvtools
VCFTOOLS ?= $(HOME)/share/usr/bin/vcftools-0.1.10
VCF_SORT ?= $(PERL) $(HOME)/share/usr/bin/vcfsorter.pl
SNP_EFF_JAR ?= $(JARDIR)/snpEff-4.3.jar
SNP_SIFT_JAR ?= $(JARDIR)/SnpSift-4.3.jar
SNP_EFF_CONFIG ?= modules/snpEff.config
#DB_NSFP ?= $(HOME)/share/reference/snpEff/dbNSFP2.4.txt.gz
DB_NSFP ?= $(HOME)/share/reference/snpEff-4.1/dbNSFP3.0b1a.hg19.txt.gz
NSFP_FIELDS ?= Uniprot_acc_Polyphen2 Uniprot_id_Polyphen2 Polyphen2_HVAR_score Polyphen2_HVAR_pred 1000Gp3_AF ESP6500_AA_AF ESP6500_EA_AF MutationAssessor_pred MutationAssessor_score MutationTaster_pred MutationTaster_score PROVEAN_pred ExAC_Adj_AF clinvar_rs clinvar_clnsig Interpro_domain
CUFFLINKS ?= cufflinks
CUFFCMP ?= cuffcompare
#SNVMIX ?= $(HOME)/share/usr/bin/SNVMix2
#BAM2FASTQ ?= $(HOME)/share/usr/bin/bam2fastq
#QUALIMAP ?= $(HOME)/share/usr/qualimap/qualimap
TOPHAT ?= tophat
DEFUSE ?= $(PERL) $(HOME)/share/usr/defuse-0.6.1/scripts/defuse.pl
#VARSCAN
ONCOFUSE_JAR ?= $(HOME)/share/usr/oncofuse-1.0.9b2/Oncofuse.jar
VARSCAN_JAR ?= $(JARDIR)/VarScan.v2.3.9.jar
# PICARD tools
PICARD_DIR ?= $(JARDIR)/picard-1.92
PICARD_JAR ?= $(JARDIR)/picard-tools-1.141/picard.jar
# scripts
SCRIPTS_DIR ?= modules/scripts
MERGE ?= $(SCRIPTS_DIR)/merge.R
VCF_TO_TABLE ?= $(SCRIPTS_DIR)/vcfToTable.R
INTRON_POSN_LOOKUP ?= $(SCRIPTS_DIR)/posnGeneLookup.pl
RBIND ?= $(SCRIPTS_DIR)/rbind.R
NORMAL_FILTER ?= $(PERL) $(SCRIPTS_DIR)/normalFilterVCF.pl
SOMATIC_FILTER_VCF ?= $(PERL) $(SCRIPTS_DIR)/somaticFilterVCF.pl
#JAVA_TMP := $(HOME)/tmp
JAVA_BIN ?= $(JAVA8_BIN)
JAVA6_BIN ?= $(HOME)/share/usr/jdk1.6.0_45/bin/java
JAVA7_BIN ?= $(HOME)/share/usr/jdk1.7.0_45/bin/java
JAVA8_BIN ?= $(HOME)/share/usr/jdk1.8.0_121/bin/java
#JAVA ?= /usr/bin/java $(JAVA_ARGS)
GET_INSERT_SIZE ?= $(HOME)/share/usr/bin/getInsertSize.py
#GATK
GATK_JAR ?= $(JARDIR)/GenomeAnalysisTK.jar
GATK_JAR2 ?= $(JARDIR)/GenomeAnalysisTK-3.7.jar
VT ?= $(HOME)/share/usr/bin/vt
TABIX ?= $(HOME)/share/usr/bin/tabix
CLUSTER_ENGINE ?= SGE
ifeq ($(CLUSTER_ENGINE),PBS)
MYSQLDB_HOST = cpu-6-2
EMBL_MYSQLDB_HOST = cpu-6-2
EMBL_MYSQLDB_PORT = 9992
EMBL_MYSQLDB_USER = embl
EMBL_MYSQLDB_PW = embl
EMBL_MYSQLDB_DB = homo_sapiens_core_85_37
endif
ifeq ($(CLUSTER_ENGINE),LSF)
MYSQLDB_HOST = lilac
EMBL_MYSQLDB_HOST = lilac
EMBL_MYSQLDB_PORT = 38493
EMBL_MYSQLDB_USER = embl
EMBL_MYSQLDB_PW = embl
EMBL_MYSQLDB_DB = homo_sapiens_core_75_37
endif
ifeq ($(CLUSTER_ENGINE),SGE)
MYSQLDB_HOST = ika
EMBL_MYSQLDB_HOST = ika
EMBL_MYSQLDB_PORT = 38493
EMBL_MYSQLDB_USER = embl
EMBL_MYSQLDB_PW = embl
EMBL_MYSQLDB_DB = homo_sapiens_core_75_37
endif
SNVBOX_CONF = $(PWD)/modules/db/snv_box-$(MYSQLDB_HOST).conf
FATHMM_CONF = $(PWD)/modules/db/fathmm_config-$(MYSQLDB_HOST).ini
INTEGRATE ?= $(HOME)/share/usr/Integrate_0.2.0/bin/Integrate
VCF2MAF ?= $(PERL) $(HOME)/share/usr/bin/vcf2maf.pl
MAF2MAF ?= $(PERL) $(HOME)/share/usr/bin/maf2maf.pl
MAF2VCF ?= $(PERL) $(HOME)/share/usr/bin/maf2vcf.pl
HISAT ?= $(HOME)/share/usr/hisat2-2.0.2-beta/hisat2
TVC ?= $(HOME)/share/usr/bin/tvc
ANNOVAR = $(PERL) $(HOME)/share/usr/annovar-2017-07-16/table_annovar.pl
ONCOTATOR_ENV = $(HOME)/share/usr/venv/oncotator-1.9.2.0
VEP_ENV = $(HOME)/share/usr/anaconda-envs/variant-effect-predictor-86
VEP_PATH = $(VEP_ENV)/bin
SPLIT_BED = python modules/scripts/split_bed.py
INDEL_FILTER_VCF = python modules/vcf_tools/indel_filter_vcf.py
SNP_FILTER_VCF = python modules/vcf_tools/snp_filter_vcf.py
MERGE_VCF = python modules/vcf_tools/merge_vcf.py
endif
CONFIG_INC = true