Makefile

#
# Makefile to streamline installation of databases
#
SHELL:=/bin/bash

PKG_NAME:=medgen-mysql

_:=$(shell mkdir -p logs)

help:
	@echo "  Type make <database> to download, unpack, create mysql store for each individual DB."
	@echo "  (for example: make clinvar)"

user: FORCE
	./create_user.sh

# NCBI ClinVar provides  "Clinical Variants" with phenotypes and gene linkages.
#              ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar
clinvar: FORCE
	rm -rf               clinvar/mirror
	-./mirror.sh         clinvar/urls
	./unpack.sh          clinvar
	make                 clinvar-xml
	./create_database.sh clinvar
	./load_database.sh   clinvar
	./index_database.sh  clinvar

# NCBI clinvar-xml : clinvar IDs to HGVS labels . 
clinvar-xml: FORCE
	pyvenv ve
	source ve/bin/activate && pip install numpy && pip install hgvs && pip install lxml
	python clinvar/clinvar_hgvs.py

# ClinVitae: public variant database aggregated by Invitae 
ClinVitae: FORCE
	rm -rf				ClinVitae/mirror
	-./mirror.sh		ClinVitae/urls
	./unpack.sh			ClinVitae
	./create_database.sh	ClinVitae
	./load_database.sh	ClinVitae
	./index_database.sh	ClinVitae

# CGD: Clinical Genomics Databsae
ClinicalGenomics: FORCE
	-./mirror.sh         ClinicalGenomics/urls
	./unpack.sh          ClinicalGenomics
	./create_database.sh ClinicalGenomics
	./load_database.sh   ClinicalGenomics
	./index_database.sh  ClinicalGenomics

# NCBI dbSNP is deliberately limited to only HGVS mappings to RS# for a full dbSNP dump
#            ftp://ftp.ncbi.nih.gov/snp
dbSNP: FORCE
	rm -rf                dbSNP/mirror
	-./mirror.sh          dbSNP/urls
	./unpack.sh           dbSNP
	./create_database.sh  dbSNP
	./load_database.sh    dbSNP
	./index_database.sh   dbSNP

# NCBI Genetic Testing Registry contains lab information for every genetic test you can order.  
#                               ftp://ftp.ncbi.nlm.nih.gov/pub/GTR/
GTR: FORCE
	-./mirror.sh         GTR/urls
	./unpack.sh          GTR
	./create_database.sh GTR
	./load_database.sh   GTR
	./index_database.sh  GTR

# GTR-xml : GTR Identifiers to PubMed citations and Testing Lab Codes (@@@TODO ) 
GTR-xml: FORCE
	virtualenv ve
	source ve/bin/activate && pip install lxml && python GTR/gtr_xml_gapfill.py

# LSDB contains BIC and LOVD installation data
# Will need to set the 
LSDB: FORCE
	rm -rf          mirror
	@if [ "${LSDB_USER}" = "" ]; then echo "Fatal error.  Need to set LSDB_USER."; exit 1; fi
	@if [ "${LSDB_PASS}" = "" ]; then echo "Fatal error.  Need to set LSDB_PASS."; exit 1; fi
	./mirror.sh    LSDB/urls.bic_breast_cancer_core
	./mirror.sh    LSDB/urls.lovd
	./unpack.sh          LSDB
	./create_database.sh LSDB
	./load_database.sh   LSDB
	./index_database.sh  LSDB

# NCBI PubTator links PubMed PMIDs to Text Mined Variants(tmVar), Genes(GenNorm), and other BioConcepts. 
#               ftp://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator
PubTator: FORCE
	rm -rf               PubTator/mirror
	-./mirror.sh         PubTator/urls
	./unpack.sh          PubTator
	./create_database.sh PubTator
	./load_database.sh   PubTator
	./index_database.sh  PubTator

# PersonalGenomes loads the MySQL dump
#                  http://evidence.pgp-hms.org
PersonalGenomes: FORCE
	-./mirror.sh         PersonalGenomes/urls
	./unpack.sh          PersonalGenomes
	./create_database.sh PersonalGenomes
	./load_database.sh   PersonalGenomes
	./index_database.sh  PersonalGenomes

#  NCBI Gene is the Entrez Gene Database 
#            ftp://ftp.ncbi.nih.gov/gene/
gene: FORCE
	rm -rf                gene/mirror
	-./mirror.sh          gene/urls
	./unpack.sh           gene
	./create_database.sh  gene
	./load_database.sh    gene
	./index_database.sh   gene

# NCBI GeneReviews provides BOOK links to Gene Names
#                  ftp://ftp.ncbi.nlm.nih.gov/pub/GeneReviews
GeneReviews: FORCE
	-./mirror.sh          GeneReviews/urls
	./unpack.sh           GeneReviews
	./create_database.sh  GeneReviews
	./load_database.sh    GeneReviews
	./index_database.sh   GeneReviews

# GO Gene Ontology is the grouping of genes 
#                  http://geneontology.org/page/download-ontology
GO: FORCE
	-./mirror.sh          GO/urls
	./unpack.sh           GO
	./create_database.sh  GO
	./load_database.sh    GO
	./index_database.sh   GO

# HUGO Gene Naming Convention provides DB links using standard gene names
#                             http://www.genenames.org/cgi-bin/download
hugo: FORCE
	-./mirror.sh          hugo/urls
	./unpack.sh           hugo
	./create_database.sh  hugo
	./load_database.sh    hugo
	./index_database.sh   hugo

# Disease Gene Network is a near-comprehensive map of Gene:Disease relationships with scoring.
#                      http://disgenet.org/web/DisGeNET/menu/downloads#all
disgenet: FORCE
	-./mirror.sh         disgenet/urls
	./unpack.sh          disgenet
	./create_database.sh disgenet
	./load_database.sh   disgenet
	./index_database.sh  disgenet 

# DECIPHER Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources
# 			Provided by Sanger: https://www.sanger.ac.uk/science/tools/decipher-mapping-clinical-genome

decipher: FORCE
	-./mirror.sh		decipher/urls
	./unpack.sh			decipher
	./create_database.sh	decipher
	./load_database.sh	decipher
	./index_database.sh	decipher

# Human Phenotype Ontology is used to associate phenotypes, even across organisms.
#                          http://human-phenotype-ontology.org
hpo: FORCE
	-./mirror.sh          hpo/urls
	./unpack.sh           hpo
	./create_database.sh  hpo
	./load_database.sh    hpo
	./index_database.sh   hpo

# Orphanet is a rare-disease ontology ( LICENSE required for commercial use)
#                              http://www.orphadata.org/
orphanet: FORCE
	-./mirror.sh         orphanet/urls

# CHV Consumer Health Vocabulary links MedGen to phrases in common language. 
#                                 http://consumerhealthvocab.org
CHV: FORCE
	-./mirror.sh         CHV/urls
	./unpack.sh          CHV
	./create_database.sh CHV
	./load_database.sh   CHV
	./index_database.sh  CHV 

# NCBI medgen links phenotypes and genes to entries in pubmed, clinvar, the genetic testing registry, and 30+ sources. 
medgen: FORCE
	-./mirror.sh         medgen/urls
	./unpack.sh          medgen
	./create_database.sh medgen
	./load_database.sh   medgen
	./index_database.sh  medgen

medgen-views: FORCE
	-cd medgen/views
	ls -lah 

# NCBI pubmed we provide links only to PubMedCentral.
#             https://www.nlm.nih.gov/databases/license/weblic/index.html  
pubmed: FORCE
	#-./mirror.sh pubmed/urls.medlinebaseline
	#-./mirror.sh pubmed/urls.medlineupdates
	#-./mirror.sh pubmed/urls.fulltext	
	-./mirror.sh         pubmed/urls.pmc	
	./unpack.sh          pubmed
	./create_database.sh pubmed
	./load_database.sh   pubmed
	./index_database.sh  pubmed

# all-variants : convenience function  
all-variants: FORCE
	make PubTator
	make  clinvar
	make  ClinVitae
	make  GTR
	-make  dbSNP
	make  PersonalGenomes

# all-genes : convenience function  
all-genes: FORCE
	-make gene
	make  GeneReviews
	make  hugo
	make  GO

# all-phenotypes : convenience function  
all-phenotypes: FORCE
	-make hpo
	make  ClinicalGenomics
	make  disgenet
	make  CHV
	make  orphanet
	make  medgen

# all : convenience function  
all: FORCE
	-make all-phenotypes
	make  all-genes
	make  all-variants
	make  pubmed	


# backup all existing databases
backup: FORCE
	-./backup_database.sh clinvar
	./backup_database.sh ClinVitae
	./backup_database.sh ClinicalGenomics
	./backup_database.sh GTR
	./backup_database.sh PubTator
	./backup_database.sh dbSNP
	./backup_database.sh PersonalGenomes
	./backup_database.sh gene
	./backup_database.sh GeneReviews
	./backup_database.sh GO
	./backup_database.sh hugo
	./backup_database.sh disgenet
	./backup_database.sh hpo
	./backup_database.sh CHV
	./backup_database.sh medgen

# clean mirror download zip contents and uncompressed files 
clean: FORCE
	-rm -rf clinvar/mirror
	rm  -rf ClinVitae/mirror
	rm  -rf ClinicalGenomics/mirror 
	rm  -rf GTR/mirror
	rm  -rf PubTator/mirror
	rm  -rf dbSNP/mirror
	rm  -rf PersonalGenomes/mirror
	rm  -rf gene/mirror
	rm  -rf GeneReviews/mirror
	rm  -rf GO/mirror
	rm  -rf hugo/mirror
	rm  -rf disgenet/mirror
	rm  -rf hpo/mirror
	rm  -rf CHV/mirror
	rm  -rf medgen/mirror
	rm  -rf pubmed/mirror

# clean ./drop_database.sh 
cleaner: clean
	-./drop_database.sh clinvar
	./drop_database.sh	ClinVitae
	./drop_database.sh  ClinicalGenomics
	./drop_database.sh  GTR
	./drop_database.sh  PubTator
	./drop_database.sh  dbSNP
	./drop_database.sh  PersonalGenomes
	./drop_database.sh  gene
	./drop_database.sh  GeneReviews
	./drop_database.sh  GO
	./drop_database.sh  hugo
	./drop_database.sh  disgenet
	./drop_database.sh  hpo
	./drop_database.sh  CHV
	./drop_database.sh  medgen
	./drop_database.sh  pubmed


# clean mirror download zip contents and uncompressed files 
cleanest: cleaner
	rm  -rf clinvar/mysqldump
	rm  -rf ClinVitae/mysqldump
	rm  -rf ClinicalGenomics/mysqldump
	rm  -rf GTR/mysqldump
	rm  -rf PubTator/mysqldump
	rm  -rf dbSNP/mysqldump
	rm  -rf PersonalGenomes/mysqldump
	rm  -rf gene/mysqldump
	rm  -rf GeneReviews/mysqldump
	rm  -rf GO/mysqldump
	rm  -rf hugo/mysqldump
	rm  -rf disgenet/mysqldump
	rm  -rf hpo/mysqldump
	rm  -rf CHV/mysqldump
	rm  -rf medgen/mysqldump
	rm  -rf pubmed/mysqldump


.PHONY:  FORCE help user all clinvar clinvarxml ClinVitae GTR gene GeneReviews GO hugo medgen orphanet PersonalGenomes pubmed PubTator dbSNP