Constants user Patrick

Documentation

These are constants commonly used by User:Kantale

Parameters

<inputs>
</inputs>

Code

def Constants_user_Patrick():
	constants_millipede = {
		"imputationtool_path" : "/data/gcc/tools/ImputationTool/dist/ImputationTool.jar",
		"path_to_impute2" : "/data/gcc/tools/impute_v2.1.2_x86_64_static/impute_v2.1.2_x86_64_static/impute2",
		"path_to_gtool" : "/data/gcc/tools/gtool_v0.6.6_x86_64/gtool",
		"path_to_plink" : "/data/gcc/tools/plink-1.07-x86_64/plink-1.07-x86_64/plink",
		"path_to_linkage2beagle" : "/data/gcc/tools/beagle_3.3_26Dec10/linkage2beagle.jar",
		"path_to_beagle" : "/data/gcc/tools/beagle_3.3_26Dec10/beagle.jar",
		"path_to_annovar" : "/data/gcc/tools/annovar_2011Jan31/annovar",
		"path_to_annovar_annotation_files_hg18" : "/data/gcc/tools/annovar_2011Jan31/annovar/humandb",
		"directory_of_reference_dataset" : "/data/gcc/resources/ImputationReferenceSets",
		"path_to_gene_ontology_36" : "/data/gcc/resources/GeneOntology/GENE_START_END_GO_FROM_ENSEMBL_36.txt",
		"path_to_gene_ontology_37" : "/data/gcc/resources/GeneOntology/GENE_START_END_GO_FROM_ENSEMBL_37.txt",		
		"pbsStats" : {
			"email" : "patrickdeelen@gmail.com",
			"queue" : "nodes",
			"nodes" : "1",	
			"ppn" : "1",
			"walltime" : "20:00:00",
			"mem" : "8gb"
		}
	}

	constants = {
		"imputationtool_path" : "/target/gpfs2/gcc/tools/ImputationTool/dist/ImputationTool2.jar",
		"path_to_impute2" : "/target/gpfs2/gcc/tools/impute_v2.1.2_x86_64_static/impute_v2.1.2_x86_64_static/impute2",
		"path_to_gtool" : "/target/gpfs2/gcc/tools/gtool_v0.6.6_x86_64/gtool",
		"path_to_plink" : "/target/gpfs2/gcc/tools/plink-1.07-x86_64/plink-1.07-x86_64/plink",
		"path_to_plink_108" : "/target/gpfs2/gcc/tools/plink-1.08/plink108",
		"path_to_fastaFromBed" : "/target/gpfs2/gcc/tools/BEDTools-Version-2.14.3/bin/fastaFromBed",
		"path_to_linkage2beagle" : "/target/gpfs2/gcc/tools/beagle_3.3_26Dec10/linkage2beagle.jar",
		"path_to_beagle2linkage" : "/target/gpfs2/gcc/tools/beagle_3.3_26Dec10/beagle2linkage.jar",
		"path_to_beagle" : "/target/gpfs2/gcc/tools/beagle_3.3_26Dec10/beagle.jar",
		"path_to_annovar" : "/target/gpfs2/gcc/tools/annovar_2011Jan31/annovar",
		"path_to_annovar_annotation_files_hg18" : "/data/gcc/tools/annovar_2011Jan31/annovar/humandb",
		"directory_of_reference_dataset" : "/data/gcc/resources/ImputationReferenceSets",
		"path_to_GATK" : "/target/gpfs2/gcc/tools/GATK-1.0.5069",
		"path_to_GATK_1_2" : "/target/gpfs2/gcc/tools/GATK-1.2-1-g33967a4/dist/GenomeAnalysisTK.jar",
		"path_to_gene_ontology_36" : "/data/gcc/resources/GeneOntology/GENE_START_END_GO_FROM_ENSEMBL_36.txt",
		"path_to_gene_ontology_37" : "/data/gcc/resources/GeneOntology/GENE_START_END_GO_FROM_ENSEMBL_37.txt",
		"path_to_liftOverVCF" : "/target/gpfs2/gcc/tools/GATK-1.0.5069/Sting/perl/liftOverVCF.pl",
		"path_to_twoBitToFa" : "/target/gpfs2/gcc/tools/twoBitToFa/twoBitToFa",
		"path_to_picard_tools" : "/target/gpfs2/gcc/tools/picard-tools-1.51",
		"path_to_samtools" : "/target/gpfs2/gcc/tools/samtools-0.1.8/samtools",
		"path_to_hg19ToHg18.over.chain" : "/target/gpfs2/gcc/resources/liftover/hg19ToHg18.over.chain",
		"path_to_hg18ToHg19.over.chain_kantale" : "/target/gpfs2/gcc/home/akanterakis/resources/hg18ToHg19.over.chain",
		"path_to_hg18ToHg19.over.chain" : "/target/gpfs2/gcc/resources/b36/chainfiles/b36ToHg19.broad.over.chain",
		"path_to_fasta_hg18" : "/target/gpfs2/gcc/home/akanterakis/resources/hg18/hg18",
		"path_to_fasta_hg18_2" : "/target/gpfs2/gcc/resources/hg18/indices/index_hg18.fa",
		"path_to_fasta_hg19" : "/target/gpfs2/gcc/home/akanterakis/resources/hg19/hg19",
		"path_to_fasta_hg19_g1k" : "/target/gpfs2/gcc/resources/hg19/indices/human_g1k_v37.fa",
		"path_to_dict_hg18" : "/target/gpfs2/gcc/home/akanterakis/resources/hg18/hg18.dict",
		"path_to_dict_hg18_2" : "/target/gpfs2/gcc/resources/hg18/indices/index_hg18.dict",
		"path_to_dict_hg19" : "/target/gpfs2/gcc/home/akanterakis/resources/hg19/hg19.dict",
		"path_to_dict_hg19_2" : "/target/gpfs2/gcc/resources/hg19/indices/index_hg19.dict",
		"path_to_vcftools" : "/target/gpfs2/gcc/tools/vcftools_0.1.6/bin/vcftools",
		"path_to_vcf_sort" : "/target/gpfs2/gcc/tools/vcftools_0.1.7/bin/vcf-sort",
		"path_to_vcf_to_tab" : "/target/gpfs2/gcc/tools/vcftools_0.1.7/perl/vcf-to-tab",
		"path_to_1000GP_20110521" : "/target/gpfs2/gcc/resources/ImputationReferenceSets/1000Genomes/vol1_ftp_release_20110521/ALL.chr@CHR@.merged_beagle_mach.20101123.snps_indels_svs.genotypes.exported.impute",
		"path_to_GoNL_pilotII" : "/target/gpfs2/gcc/resources/ImputationReferenceSets/GoNL/hg19/gonl.pilot2.vqsr.v1.2.chr@CHR@.bgl.phased.impute",
		"path_to_genetic_map_b36" : "/target/gpfs2/gcc/resources/ImputationReferenceSets/hapmap3_r2_b36_from_impute2/hapmap3_r2_b36/genetic_map_chr@CHR@_combined_b36.txt",
		"path_to_genetic_map_b37" : "/target/gpfs2/gcc/resources/ImputationReferenceSets/1000Genomes/Phase_I_interim_b37_impute2_Jun_2011/ALL_1000G_phase1interim_jun2011_impute/genetic_map_chr@CHR@_combined_b37.txt",
		"pbsStats" : {
			"email" : "alexandros.kanterakis@gmail.com",
			"queue" : "gcc",
			"nodes" : "1",
			"ppn" : "1",
			"walltime" : "20:00:00",
			"mem" : "8gb"
		}
	}

	return constants

Unit Tests

def uni1():
	return True

Development Code

def Constants_user_Patrick():
	pass

Permissions

Documentation Permissions

Patrick

Code Permissions

Patrick

Unit Tests Permissions

Patrick

Permissions Permissions

Patrick