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importer.properties
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importer.properties
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# importer database settings
db.user=
db.password=
db.host=
db.portal_db_name=
db.importer_db_name=
db.driver=com.mysql.jdbc.Driver
db.connection_string=jdbc:mysql://localhost/
db.portal_schema=$PORTAL_HOME/core/src/main/resources/db/cgds.sql
# vep
annotator.maf2maf=/opt/common/CentOS_6/vcf2maf/v1.6.2/maf2maf.pl
annotator.vcf2maf=/opt/common/CentOS_6/vcf2maf/v1.6.2/vcf2maf.pl
annotator.perl_bin=/opt/common/CentOS_6-dev/perl/perl-5.22.0/bin/perl
annotator.perl_lib=PERL5LIB=/opt/common/CentOS_6-dev/perl/perl-5.22.0/lib/5.22.0:/opt/common/CentOS_6-dev/perl/perl-5.22.0/lib/perl5:/opt/common/CentOS_6-dev/perl/perl-5.22.0/lib/perl5/x86_64-linux
annotator.vep_path=/opt/common/CentOS_6/vep/v81
annotator.vep_data=/opt/common/CentOS_6/vep/v81
annotator.ref_fasta=/ssd-data/cmo/opt/vep/v79/homo_sapiens/79_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
annotator.exclude_cols=oncotator
annotator.mode=regular
annotator.intermediate_maf=annotator_out.maf
annotator.vep_forks=32
annotator.tmp_dir=/ssd-data/vep-tmp/ben
annotator.path=PATH=/opt/common/CentOS_6-dev/perl/perl-5.22.0/bin/:/ssd-data/cmo/bin
annotator.cluster_node=
annotator.cluster_sp=
annotator.custom_enst=/opt/common/CentOS_6/vcf2maf/v1.6.2/data/isoform_overrides_at_mskcc
# google docs credentials
google.id=
google.pw=
# google docs portal importer configuration worksheet
importer.google.service.private.key.file=
importer.google.service.email=
importer.spreadsheet_service_appname=cBio Portal Importer Tool
importer.spreadsheet=portal_importer_configuration_tcga
importer.cancer_studies_worksheet=cancer_studies
importer.case_id_filters_worksheet=case_id_filters
importer.case_lists_worksheet=case_lists
importer.clinical_attributes_namespace_worksheet=clinical_attributes_namespace
importer.clinical_attributes_worksheet=clinical_attributes
importer.datatypes_worksheet=datatypes
importer.data_sources_worksheet=data_sources
importer.portals_worksheet=portals
importer.reference_data_worksheet=reference_data
importer.tcga_tumor_types_worksheet=tcga_tumor_types
importer.oncotree_worksheet=oncotree_src
importer.oncotree_properties_worksheet=oncotree_properties
# firehose_get script
firehose_get_script=$PORTAL_HOME/importer/src/main/scripts/firehose_get
# liftover tool filepaths
liftover_binary=
liftover_chain_file=
# clinical data
supply_default_clinical_attribute_values=true
tcga.clinical.url=https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<TUMOR_TYPE>/bcr/nationwidechildrens.org/bio/clin/|https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<TUMOR_TYPE>/bcr/genome.wustl.edu/bio/clin/
tcga.clinical.filename=nationwidechildrens.org_<TUMOR_TYPE>.bio.Level_2.0.<REVISION>.0.tar.gz|genome.wustl.edu_<TUMOR_TYPE>.bio.Level_2.0.<REVISION>.0.tar.gz
nci.cadsr.url=http://cadsrapi.nci.nih.gov/cadsrapi40/GetXML?query=
nci.cadsr.query=DataElement[@publicId=CDE_ID:]
# mail
mail.server=localhost
mail.triage_portal.update.message.sender=
mail.triage_portal.update.message.recipient=
mail.triage_portal.update.message.subject=
mail.triage_portal.update.message.body=
mail.msk_portal.update.message.sender=
mail.msk_portal.update.message.recipient=
mail.msk_portal.update.message.subject=
mail.msk_portal.update.message.body=
mail.redeploy.message.sender=
mail.redeploy.message.recipient=
mail.redeploy.message.subject=
mail.redeploy.message.body=
# sftp on production server (for redeploy war)
production.sftp.host=
production.sftp.username=
production.sftp.password=