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Makefile.common
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Makefile.common
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# common makefile holding variables needed by all makefiles.
# First, we import secured variables
include $(PIPELINEROOT)Makefile.Config
# Force bash because we use bash constructions in Makefiles and default Makefile shell on Ubuntu is /bin/sh (different from /bin/bash)
SHELL = /bin/bash
.PHONY: all clean
# ===================================
# GENERAL PARAMETERS
# ===================================
MAJOR_RELEASE := 16
MINOR_RELEASE := 0
RELEASE := $(MAJOR_RELEASE).$(MINOR_RELEASE)
# MySQL database connection parameters
# DBUSER and DBPASS defined in Makefile.Config
# DBUSERV and DBPASSV defined in Makefile.Config
DBNAME := bgee_v$(subst .,_,$(RELEASE))
DBHOST := dbbioinfo.unil.ch
DBPORT := 3306
DBNAME_EASYBGEE := easybgee_v$(subst .,_,$(RELEASE))
DBHOST_EASYBGEE := localhost
# Pipeline container
PIPELINE_CONTAINER_NAME := BgeePipeline
PIPELINE_CONTAINER_RELEASE := 0
PIPELINE_CONTAINER_FILE := $(PIPELINE_CONTAINER_NAME)-$(RELEASE).$(PIPELINE_CONTAINER_RELEASE).sif
PIPELINE_CONTAINER_CMD := apptainer exec $(PIPELINE_CONTAINER_FILE)
# Annotator machine
# ANNOTATORLOGIN defined in Makefile.Config
ANNOTATORHOST := annotbioinfo.unil.ch
# Cluster account
# CLUSTERLOGIN and CLUSTERPASSW defined in Makefile.Config
CLUSTERHOST := curnagl.dcsr.unil.ch
# Machine used for the pipeline
# PIPELOGIN and PIPEPASSWD defined in Makefile.Config
PIPEHOST := devbioinfo.unil.ch
# Machine used for RNA-seq/Affymetrix data transfer
# DATALOGIN and DATAPASSWD defined in Makefile.Config
DATAHOST := jura0.sib.swiss
DATAPATH := /data
# Ensembl
ENSRELEASE := 112
ENSMETAZOARELEASE := 59
ENS_API_RELEASE := $(ENSRELEASE)
ENSMETAZOA_API_RELEASE := $(ENSRELEASE)
# Default, remote Ensembl db
# see https://www.ensembl.org/info/data/mysql.html
ENSDBUSER := anonymous
ENSDBPASS := ''
ENSDBHOST := ensembldb.ensembl.org
ENSDBPORT := 5306
# Default, remote Ensembl genomes db
# see https://metazoa.ensembl.org/info/data/mysql.html
ENSGDBHOST := mysql-eg-publicsql.ebi.ac.uk
ENSGDBPORT := 4157
# local BDGP
BDGPDBNAME := bdgp
# Bgee connection command line argument for Perl scripts
BGEECMD := user=$(DBUSER)__pass=$(DBPASS)__host=$(DBHOST)__port=$(DBPORT)__name=$(DBNAME)
BGEECMDV := user=$(DBUSERV)__pass=$(DBPASSV)__host=$(PIPEHOST)__port=$(DBPORT)__name=$(DBNAME)
# Ensembl connection command line argument for Perl scripts
ENSCMD := user=$(ENSDBUSER)__pass=$(ENSDBPASS)__host=$(ENSDBHOST)__port=$(ENSDBPORT)
# BDGP connection command line argument for Perl scripts
BDGPCMD := user=$(DBUSER)__pass=$(DBPASS)__host=$(DBHOST)__port=$(DBPORT)__name=$(BDGPDBNAME)
# ===================================
# COMMANDS
# ===================================
JAVALIBDIR := ../java/
BGEEPIPELINEJARNAME := bgee-pipeline-$(RELEASE)-with-dependencies.jar
BGEEPIPELINEJAR := $(JAVALIBDIR)$(BGEEPIPELINEJARNAME)
# --add-opens java.base/java.lang=ALL-UNNAMED: see https://stackoverflow.com/a/77874779/1768736
JAVA_NO_JAR := java -Xmx150g -Dbgee.dao.jdbc.username=$(DBUSER) -Dbgee.dao.jdbc.password=$(DBPASS) -Dbgee.dao.jdbc.driver.names=com.mysql.cj.jdbc.Driver,net.sf.log4jdbc.sql.jdbcapi.DriverSpy -Dbgee.dao.jdbc.url='jdbc:log4jdbc:mysql://$(DBHOST):$(DBPORT)/$(DBNAME)?useSSL=false&allowPublicKeyRetrieval=True&enableQueryTimeouts=false&sessionVariables=net_write_timeout=260000,net_read_timeout=260000,wait_timeout=260000' --add-opens java.base/java.lang=ALL-UNNAMED
# Java command allowing to connect to easyBgee without Jar. Never used without JAR for the moment but created to follow the same pattern than JAVA_NO_JAR/JAVA variables for Bgee
JAVA_NO_JAR_EASYBGEE := java -Xmx64g -Dbgee.dao.jdbc.username=$(DBUSER_EASYBGEE) -Dbgee.dao.jdbc.password=$(DBPASS_EASYBGEE) -Dbgee.dao.jdbc.driver.names=com.mysql.cj.jdbc.Driver,net.sf.log4jdbc.sql.jdbcapi.DriverSpy -Dbgee.dao.jdbc.url='jdbc:log4jdbc:mysql://$(DBHOST_EASYBGEE):$(DBPORT)/$(DBNAME_EASYBGEE)?useSSL=false&allowPublicKeyRetrieval=True&enableQueryTimeouts=false&sessionVariables=net_write_timeout=500000,net_read_timeout=500000,wait_timeout=500000'
JAVA := $(JAVA_NO_JAR) -jar $(PIPELINEROOT)$(BGEEPIPELINEJAR)
JAVA_EASYBGEE := $(JAVA_NO_JAR_EASYBGEE) -jar $(PIPELINEROOT)$(BGEEPIPELINEJAR)
# to pass arguments to Java command line
ENTRY_SEP :=,
KEY_VAL_SEP :=//
VAL_SEP :=--
EMPTY_LIST :=-
LIST_SEP :=,
SPACE :=__
MYSQLNODBNAME := mysql -u $(DBUSER) -p$(DBPASS) -h $(DBHOST) -P $(DBPORT) --init-command='SET SESSION net_write_timeout=260000; SET SESSION net_read_timeout=260000; SET SESSION wait_timeout=260000'
MYSQL := $(MYSQLNODBNAME) $(DBNAME)
MYSQLNODBNAME_EASYBGEE := mysql -u $(DBUSER_EASYBGEE) -p$(DBPASS_EASYBGEE) -h $(DBHOST_EASYBGEE) -P $(DBPORT) --init-command='SET SESSION net_write_timeout=86400; SET SESSION net_read_timeout=86400; SET SESSION wait_timeout=86400'
MYSQL_EASYBGEE := $(MYSQLNODBNAME_EASYBGEE) $(DBNAME_EASYBGEE)
GIT := git
WGET := wget -N -nv
#RSYNC := rsync -a --exclude=.DS_Store # some permission problems so don't strickly speaking use -a (== -rlptgoD)
RSYNC := rsync -rlgoD --exclude=.DS_Store --exclude=.svn --exclude=.git
CAT := cat
RM := rm -f
MV := mv -f
CP := cp -f
GUNZIP := gunzip -f
MKDIR := mkdir -p
LC_ALL = 'C'
PYTHON3 = python3
PIPENV = pipenv
# cURL command, to download files only if more recently changed
# (it was not working correctly with wget in our case)
# -s: silent, no progress bar displayed;
# -S: if silent, still shows error message if it fails;
# -L: in case of redirection, follow it and redo the request, this is necessary to correctly get modification date;
# -f: in case of error do not display the document returned.
# -R: make the local file have the same timestamp as remote file
# Sould be used with option -z filename: download remote file only if more recent than the provided file
# And with -o option to choose output file name.
# See variable APPEND_CURL_COMMAND.
CURL := curl -s -S -L -f -R
# variable to append to cURL command to download a file only if remote file more recent than targeted file,
# download in a temp file and move to stable location on success; delete temp file on error
# Variable to be recursively expanded.
# -z filename: download remote file only if last modification date more recent that modification date of downloadfile
# -o filename: store downloaded file into filename
# Redirect stderr of mv to /dev/null in case the file was not redownloaded so that the temp file does not exist
APPEND_CURL_COMMAND = -z $@ -o $@.tmp && mv -f $@.tmp $@ 2>/dev/null || rm -f $@.tmp $@
# Paths to files used in several Makefiles, relative to the Makefile pipeline root (bgee/pipeline/pipeline)
# Needs to be included after we defined some variables used in the file
include $(PIPELINEROOT)Makefile.taxon_info
# ===================================
# CLUSTER COMMANDS
# ===================================
CLUSTER_DATA_PATH := /data/FAC/FBM/DEE/mrobinso/bgee_sensitive
# use the /data folder to avoid providing user scratch directory as there is currently no project scratch directory
CLUSTER_SCRATCH_PATH := $(CLUSTER_DATA_PATH)
CLUSTER_SCRATCH_RESULTS := $(CLUSTER_SCRATCH_PATH)/$(DBNAME)/
CLUSTER_ARCHIVE_PATH := /archive/FAC/FBM/DEE/mrobinso/bgee_sensitive
CLUSTER_CURNAGL_PATH := /work/FAC/FBM/DEE/mrobinso/bgee/
CLUSTER_TOOLS_DIR := $(CLUSTER_CURNAGL_PATH)/tools/
R_LIBS_PATH_SENSITIVE := $(CLUSTER_DATA_PATH)/R_LIBS
R_LIBS_PATH_CURNAGL := $(CLUSTER_CURNAGL_PATH)/R_LIBS
PERL_LIBS_PATH_CURNAGL := $(CLUSTER_CURNAGL_PATH)/PERL_LIBS/lib/perl5
#NOTE Think to add ; at the end to ease insertion in other command lines
CLUSTER_SOFT_VITALIT := module use /software/module/;
CLUSTER_SOFT_UNIL := module load gcc/10.4.0;
CLUSTER_KALLISTO_CMD := $(CLUSTER_SOFT_VITALIT) module load UHTS/Analysis/kallisto/0.46.0;
CLUSTER_R_CMD := $(CLUSTER_SOFT_VITALIT) module load R/3.6.1;
CLUSTER_R_CMD2 := $(CLUSTER_SOFT_UNIL) module load r/4.0.5;
CLUSTER_ENSEMBL_API := module load Development/Ensembl_API/97;
CLUSTER_SOFTWARE_BIN := export PATH=/software/bin:$$PATH;
SENSITIVE_PERL_CMD := $(CLUSTER_SOFT_VITALIT) $(CLUSTER_ENSEMBL_API) $(CLUSTER_SOFTWARE_BIN)
CLUSTER_PERL_CMD := $(CLUSTER_SOFT_UNIL) module load perl/5.32.1;
CLUSTER_SRATOOLKIT_CMD := $(CLUSTER_SOFT_UNIL) module load sratoolkit/2.10.9;
CLUSTER_TOPHAT_CMD := $(CLUSTER_SOFT_VITALIT) module load UHTS/Aligner/tophat/2.1.1;
CLUSTER_FASTP_CMD := $(CLUSTER_SOFT_UNIL) module load fastp/0.23.2;
CLUSTER_BUSTOOLS_CMD := $(CLUSTER_SOFT_VITALIT) module load UHTS/Analysis/bustools/0.40.0;
# ===================================
# PATHS TO FILES
# ===================================
# Tmp path (if not enough disk space)
TMPDIR := /var/lib/mysql/tmp/bgee_v15_2/
# Path to the directory storing source files
# PIPELINEROOT and DIR_NAME are specified by each individul Makefile
# before importing Makefile.common
SOURCE_FILES_DIR := $(PIPELINEROOT)../source_files/
INPUT_DIR := $(SOURCE_FILES_DIR)$(DIR_NAME)
ANNOT_SUBMODULE_DIR := $(SOURCE_FILES_DIR)bgee-expression-annotations.git/
GENERATED_FILES_DIR := $(PIPELINEROOT)../generated_files/
OUTPUT_DIR := $(GENERATED_FILES_DIR)$(DIR_NAME)
VERIFICATIONFILE := $(OUTPUT_DIR)step_verification_$(RELEASE).txt
# =========== FILES FROM ANNOTATORS ===============
# URL to git annotation files
#ANNOTATION_GIT_URL := https://gitlab.sib.swiss/Bgee/expression-annotations/tree/develop
# Directory with curator files, from the root directory of the pipeline
#CURATIONPATH := ../../curation/
## AFFYMETRIX
#AFFY_CURATION_PATH := $(CURATIONPATH)expression_data/affymetrix/
#AFFY_CURATION_FILEPATH := $(AFFY_CURATION_PATH)annotation.xls
## SIMILARITY
#SIMILARITY_CURATION_PATH := $(CURATIONPATH)similarity/
#SIMILARITY_CURATION_FILEPATH := $(SIMILARITY_CURATION_PATH)homology.xlsx
## ESTs
#EST_CURATION_PATH := $(CURATIONPATH)expression_data/est/
#EST_UNIGENE_CURATION_PATH := $(EST_CURATION_PATH)unigene/
#EST_SMIRNADB_CURATION_PATH := $(EST_CURATION_PATH)smirnadb/
# the list of species with UniGene/EST annotation
EST_SPECIES_CURATION_FILEPATH := $(SOURCE_FILES_DIR)ESTs/unigene/species_EST_file.txt
# smiRNAdb libs mapping file
SMIRNADB_CURATION_MAPFILEPATH := $(SOURCE_FILES_DIR)ESTs/smirnadb/mapping_libs_smiRNAdb.csv
## In Situ
#BDGP_PATH := $(CURATIONPATH)expression_data/in_situ/bdgp/
BDGP2FBBT_MAPPING_FILE := BDGP_terms_to_FBbt_terms.tsv
BDGP2FBBT_MAPPING_NEW := BDGP_terms_to_FBbt_terms_$(DBNAME).tsv
STAGECORRESP_FILE := BDGP_stages_correspondence.txt
WORMBASE_EXPR_DUMP := expr_pattern.ace
## RNA Seq
#RNASEQ_CURATION_PATH := $(CURATIONPATH)expression_data/rna_seq/
#RNASEQ_CURATION_FILEPATH := $(RNASEQ_CURATION_PATH)annotations.xls
# =========== SPECIES FILES ===============
# a TSV file containing the IDs of the species used in Bgee
SPECIESFILEPATH := $(SOURCE_FILES_DIR)species/bgeeSpecies.tsv
# file containing the IDs of all the taxa used in our annotations
ANNOTTAXIDSFILEPATH := $(GENERATED_FILES_DIR)species/annotTaxIds.tsv
# file containing the IDs of the species used in Bgee, of all the taxa used in our annotations,
# and of all the taxa used in Uberon
ALLTAXIDSFILEPATH := $(GENERATED_FILES_DIR)species/allTaxIds.tsv
# our custom taxonomy ontology
TAXONOMYFILEPATH := $(GENERATED_FILES_DIR)species/bgee_ncbitaxon.owl
TAX_DAT_DOWNLOAD_URL := ftp://ftp.ebi.ac.uk/pub/databases/taxonomy/taxonomy.dat
# =========== GENE FILES ===============
HOMOLOGS_DIR := $(OUTPUT_DIR)homologs
PARALOGS_DIR := $(OUTPUT_DIR)paralogs/
ORTHOLOGS_DIR := $(OUTPUT_DIR)orthologs/
XREFS_FROM_UNIPROT_FILE := $(OUTPUT_DIR)xrefs_from_uniprot.tsv
#Where config files will be saved, these files are also used by the orthologs/paralogs app
#to restart from where it stopped in a previous execution or to execute it incrementally.
TEMPORARY_CONFIG_FILES_DIR = $(OUTPUT_DIR)temp
#The homology pairwise application directory and main file
GENERATE_HOMOLOGS_APP_DIR = $(PIPELINEROOT)genes/orthologs_paralogs_app
GENERATE_HOMOLOGS_APP_FILE = $(GENERATE_HOMOLOGS_APP_DIR)/GenerateHomologsParallelApp.py
#For the below CSV files, each species is in a new line and represented with its NCBI identifier
#The 1st line is ignored (i.e. heading).
#A csv file containing all wanted species to get orthologs and paralogs
ALL_SPECIES_FILE = $(GENERATE_HOMOLOGS_APP_DIR)/species_lists/all_speciesId.csv
#A csv file containing exclusively the NCBI species to get orthologs and paralogs
ONLY_NCBI_SPECIES_FILE = $(GENERATE_HOMOLOGS_APP_DIR)/species_lists/ncbi_speciesId.csv
#A csv file containing exclusively the FlyBASE species to get orthologs and paralogs
ONLY_FLYBASE_SPECIES_FILE = $(GENERATE_HOMOLOGS_APP_DIR)/species_lists/flybase_speciesId.csv
#the URL or file path that contains ncbi gene ids mappings to ensembl gene ids
NCBI_GENE2ENSEMBL_URL := https://ftp.ncbi.nih.gov/gene/DATA/gene2ensembl.gz
# =========== UBERON FILES ===============
UBERON_SOURCE_PATH := $(SOURCE_FILES_DIR)uberon/
UBERON_OUTPUT_PATH := $(GENERATED_FILES_DIR)uberon/
UBERON_DOWNLOAD_URL_START := http://purl.obolibrary.org/obo/uberon/
EXT_DOWNLOAD_URL := $(UBERON_DOWNLOAD_URL_START)ext.owl
COMPOSITE_DOWNLOAD_URL := $(UBERON_DOWNLOAD_URL_START)composite-metazoan.owl
DEV_STAGE_DOWNLOAD_URL := https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/external/bgee/dev_stage_ontology.obo
# Sex-related info about anatomical terms
UBERON_SEX_INFO_FILE := uberon_sex_info.tsv
UBERON_SEX_INFO_FILE_PATH := $(UBERON_OUTPUT_PATH)$(UBERON_SEX_INFO_FILE)
# taxon constraints
TAXONCONSTRAINTSFILE := taxonConstraints.tsv
TAXONCONSTRAINTSFILEPATH := $(UBERON_OUTPUT_PATH)$(TAXONCONSTRAINTSFILE)
# OVERRIDE_TAXON_CONSTRAINTS := HsapDv:$(KEY_VAL_SEP)9606$(ENTRY_SEP)MmusDv:$(KEY_VAL_SEP)10090$(ENTRY_SEP)ZFS:$(KEY_VAL_SEP)7955$(ENTRY_SEP)XAO:$(KEY_VAL_SEP)8364$(ENTRY_SEP)FBdv:$(KEY_VAL_SEP)7227$(ENTRY_SEP)GgalDv:$(KEY_VAL_SEP)9031$(ENTRY_SEP)GgorDv:$(KEY_VAL_SEP)9593$(ENTRY_SEP)MmulDv:$(KEY_VAL_SEP)9544$(ENTRY_SEP)MdomDv:$(KEY_VAL_SEP)13616$(ENTRY_SEP)OanaDv:$(KEY_VAL_SEP)9258$(ENTRY_SEP)PtroDv:$(KEY_VAL_SEP)9598$(ENTRY_SEP)PpanDv:$(KEY_VAL_SEP)9597$(ENTRY_SEP)PpygDv:$(KEY_VAL_SEP)9600$(ENTRY_SEP)BtauDv:$(KEY_VAL_SEP)9913$(ENTRY_SEP)RnorDv:$(KEY_VAL_SEP)10116$(ENTRY_SEP)AcarDv:$(KEY_VAL_SEP)28377$(ENTRY_SEP)TnigDv:$(KEY_VAL_SEP)99883$(ENTRY_SEP)SscrDv:$(KEY_VAL_SEP)9823$(ENTRY_SEP)WBls:$(KEY_VAL_SEP)6239$(ENTRY_SEP)UBERON:0007220$(KEY_VAL_SEP)7227$(VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0004707$(KEY_VAL_SEP)7955$(ENTRY_SEP)UBERON:0000069$(KEY_VAL_SEP)6239$(VAL_SEP)7227$(VAL_SEP)7955$(VAL_SEP)8364$(ENTRY_SEP)UBERON:0000070$(KEY_VAL_SEP)7227$(ENTRY_SEP)UBERON:0000111$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)8364$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0000110$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)8364$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0000107$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(ENTRY_SEP)UBERON:0000108$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(ENTRY_SEP)UBERON:0000106$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(ENTRY_SEP)UBERON:0004729$(KEY_VAL_SEP)6239$(ENTRY_SEP)UBERON:0004730$(KEY_VAL_SEP)7227$(ENTRY_SEP)UBERON:0007234$(KEY_VAL_SEP)7955$(VAL_SEP)8364$(ENTRY_SEP)UBERON:0007232$(KEY_VAL_SEP)7955$(VAL_SEP)8364$(ENTRY_SEP)UBERON:0000112$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0000113$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0009849$(KEY_VAL_SEP)8364$(ENTRY_SEP)UBERON:0014405$(KEY_VAL_SEP)$(EMPTY_LIST)$(ENTRY_SEP)UBERON:0014862$(KEY_VAL_SEP)$(EMPTY_LIST)$(ENTRY_SEP)UBERON:0014864$(KEY_VAL_SEP)$(EMPTY_LIST)$(ENTRY_SEP)UBERON:0007221$(KEY_VAL_SEP)9606$(VAL_SEP)10090$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9031$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)13616$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)9913$(VAL_SEP)28377$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0007222$(KEY_VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)UBERON:0018241$(KEY_VAL_SEP)10090$(VAL_SEP)7955$(VAL_SEP)8364$(VAL_SEP)7227$(VAL_SEP)9593$(VAL_SEP)9544$(VAL_SEP)9258$(VAL_SEP)9598$(VAL_SEP)9597$(VAL_SEP)9600$(VAL_SEP)99883$(VAL_SEP)9823$(VAL_SEP)6239$(VAL_SEP)10116$(ENTRY_SEP)AAO:$(KEY_VAL_SEP)8364$(ENTRY_SEP)ABA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)EHDAA2:$(KEY_VAL_SEP)9606$(ENTRY_SEP)EMAPA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)FBbt:$(KEY_VAL_SEP)7227$(ENTRY_SEP)FMA:$(KEY_VAL_SEP)9606$(ENTRY_SEP)HAO:$(KEY_VAL_SEP)7399$(ENTRY_SEP)MA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)MFO:$(KEY_VAL_SEP)8089$(ENTRY_SEP)SPD:$(KEY_VAL_SEP)6893$(ENTRY_SEP)TADS:$(KEY_VAL_SEP)6939$(ENTRY_SEP)TAO:$(KEY_VAL_SEP)7955$(VAL_SEP)99883$(ENTRY_SEP)TGMA:$(KEY_VAL_SEP)44484$(ENTRY_SEP)WBbt:$(KEY_VAL_SEP)6239$(ENTRY_SEP)XAO:$(KEY_VAL_SEP)8364$(ENTRY_SEP)ZFA:$(KEY_VAL_SEP)7955$(ENTRY_SEP)EHDAA:$(KEY_VAL_SEP)9606$(ENTRY_SEP)EV:$(KEY_VAL_SEP)9606
# taxon constraints with no hacks:
# OVERRIDE_TAXON_CONSTRAINTS := HsapDv:$(KEY_VAL_SEP)9606$(ENTRY_SEP)MmusDv:$(KEY_VAL_SEP)10090$(ENTRY_SEP)ZFS:$(KEY_VAL_SEP)7955$(ENTRY_SEP)XAO:$(KEY_VAL_SEP)8364$(ENTRY_SEP)FBdv:$(KEY_VAL_SEP)7227$(ENTRY_SEP)GgalDv:$(KEY_VAL_SEP)9031$(ENTRY_SEP)GgorDv:$(KEY_VAL_SEP)9593$(ENTRY_SEP)MmulDv:$(KEY_VAL_SEP)9544$(ENTRY_SEP)MdomDv:$(KEY_VAL_SEP)13616$(ENTRY_SEP)OanaDv:$(KEY_VAL_SEP)9258$(ENTRY_SEP)PtroDv:$(KEY_VAL_SEP)9598$(ENTRY_SEP)PpanDv:$(KEY_VAL_SEP)9597$(ENTRY_SEP)PpygDv:$(KEY_VAL_SEP)9600$(ENTRY_SEP)BtauDv:$(KEY_VAL_SEP)9913$(ENTRY_SEP)RnorDv:$(KEY_VAL_SEP)10116$(ENTRY_SEP)AcarDv:$(KEY_VAL_SEP)28377$(ENTRY_SEP)TnigDv:$(KEY_VAL_SEP)99883$(ENTRY_SEP)SscrDv:$(KEY_VAL_SEP)9823$(ENTRY_SEP)WBls:$(KEY_VAL_SEP)6239$(ENTRY_SEP)PdumDv:$(KEY_VAL_SEP)6358$(ENTRY_SEP)UBERON:0000069$(KEY_VAL_SEP)6239$(VAL_SEP)7227$(VAL_SEP)7955$(VAL_SEP)8364$(ENTRY_SEP)AAO:$(KEY_VAL_SEP)8364$(ENTRY_SEP)ABA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)EHDAA2:$(KEY_VAL_SEP)9606$(ENTRY_SEP)EMAPA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)FBbt:$(KEY_VAL_SEP)7227$(ENTRY_SEP)FMA:$(KEY_VAL_SEP)9606$(ENTRY_SEP)HAO:$(KEY_VAL_SEP)7399$(ENTRY_SEP)MA:$(KEY_VAL_SEP)10090$(ENTRY_SEP)MFO:$(KEY_VAL_SEP)8089$(ENTRY_SEP)SPD:$(KEY_VAL_SEP)6893$(ENTRY_SEP)TADS:$(KEY_VAL_SEP)6939$(ENTRY_SEP)TAO:$(KEY_VAL_SEP)7955$(VAL_SEP)99883$(ENTRY_SEP)TGMA:$(KEY_VAL_SEP)44484$(ENTRY_SEP)WBbt:$(KEY_VAL_SEP)6239$(ENTRY_SEP)ZFA:$(KEY_VAL_SEP)7955$(ENTRY_SEP)EHDAA:$(KEY_VAL_SEP)9606$(ENTRY_SEP)EV:$(KEY_VAL_SEP)9606$(ENTRY_SEP)CEPH:$(KEY_VAL_SEP)6605$(ENTRY_SEP)CTENO:$(KEY_VAL_SEP)10197$(ENTRY_SEP)PORO:$(KEY_VAL_SEP)6040
STAGETAXONCONSTRAINTSFILE := stageTaxonConstraints.tsv
STAGETAXONCONSTRAINTSFILEPATH := $(UBERON_OUTPUT_PATH)$(STAGETAXONCONSTRAINTSFILE)
ROOTS_OF_SUBGRAPHS_TO_IGNORE := NCBITaxon:1
CELL_TYPE_ROOT_ID := GO:0005575
## Uberon
UBERON_EXT_FILE_PATH := $(UBERON_SOURCE_PATH)ext.owl
UBERON_COMPOSITE_FILE_PATH := $(UBERON_SOURCE_PATH)composite-metazoan.owl
UBERONFILE := $(UBERON_COMPOSITE_FILE_PATH)
UBERONFILEPATH := $(UBERON_SOURCE_PATH)$(UBERONFILE)
CUSTOM_UBERON_PREFIX := custom_composite
CUSTOM_UBERON_FILE := $(CUSTOM_UBERON_PREFIX).owl
CUSTOM_UBERON_FILE_PATH := $(UBERON_OUTPUT_PATH)$(CUSTOM_UBERON_FILE)
DEV_STAGE_ONT_PREFIX := dev_stage_ontology
DEV_STAGE_ONT_FILE := $(DEV_STAGE_ONT_PREFIX).obo
DEV_STAGE_ONT_FILE_PATH := $(UBERON_SOURCE_PATH)$(DEV_STAGE_ONT_FILE)
## Strains
STRAINS := Strains/
STRAIN_MAPPING_FILE := $(SOURCE_FILES_DIR)$(STRAINS)StrainMapping.tsv
# Command to get list of stages between start and end stages
# Missing arguments are SPECIES_ID INBETWEENSTAGESPORT
INBETWEENSTAGESPORT := 15444
INBETWEENSTAGES := $(JAVA) UberonSocketTool stageRange $(DEV_STAGE_ONT_FILE_PATH) $(TAXONOMYFILEPATH) $(STAGETAXONCONSTRAINTSFILEPATH)
# Command to get mapping of IDs to Uberon
# Missing arguments is: IDMAPPINGPORT
IDMAPPINGPORT := 14555
# Note: was changed to use our custom version with only terms included in Bgee
IDMAPPING := $(JAVA) UberonSocketTool idMapping $(CUSTOM_UBERON_FILE_PATH)
STGMAPPINGPORT := 13222
STGMAPPING := $(JAVA) UberonSocketTool idMapping $(DEV_STAGE_ONT_FILE_PATH)
# =========== SIMILARITY ANNOTATION FILES ===============
RAW_SIMILARITY_FILE := $(SOURCE_FILES_DIR)annotations/raw_similarity_annotations.tsv
SUMMARY_SIMILARITY_FILE := $(SOURCE_FILES_DIR)annotations/summary_similarity_annotations.tsv
# =========== EST FILES ===============
# =========== AFFYMETRIX FILES ===============
AFFYPATH := Affymetrix/
AFFY_CHIP_FILEPATH := $(SOURCE_FILES_DIR)$(AFFYPATH)affymetrixChip.tsv
AFFY_CHIP_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(AFFYPATH)affymetrixChip_worm.tsv
AFFY_CHIP_FILEPATH_FULL := $(GENERATED_FILES_DIR)$(AFFYPATH)affymetrixChip_full.tsv
AFFY_CHIPINFO_FILEPATH := $(GENERATED_FILES_DIR)$(AFFYPATH)affymetrixChipInformation
MICROARRAY_EXPERIMENT_FILEPATH := $(SOURCE_FILES_DIR)$(AFFYPATH)microarrayExperiment.tsv
MICROARRAY_EXPERIMENT_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(AFFYPATH)microarrayExperiment_worm.tsv
MICROARRAY_EXPERIMENT_FILEPATH_FULL := $(GENERATED_FILES_DIR)$(AFFYPATH)microarrayExperiment_full.tsv
AFFY_CHIPTYPE_FILEPATH := $(SOURCE_FILES_DIR)$(AFFYPATH)chipType.tsv
AFFY_CHIPTYPE_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(AFFYPATH)chipType_worm.tsv
AFFY_CHIPTYPE_FILEPATH_FULL := $(GENERATED_FILES_DIR)$(AFFYPATH)chipType_full.tsv
AFFY_CHIPTYPEQUAL_FILEPATH := $(GENERATED_FILES_DIR)$(AFFYPATH)chipTypeCorrespondencesAndQualityThresholds
AFFY_NORMTYPE_FILEPATH := $(GENERATED_FILES_DIR)$(AFFYPATH)normalizationType
AFFY_DETCTYPE_FILEPATH := $(GENERATED_FILES_DIR)$(AFFYPATH)detectionType
# Affymetrix data path
#AFFYDATAPATH := $(CLUSTER_DATA_PATH)/Affymetrix_v$(MAJOR_RELEASE)/
AFFYDATAPATH := /var/bgee/extra/pipeline/Affymetrix_v$(MAJOR_RELEASE)/
AFFYNEWDATAPATH := $(AFFYDATAPATH)new_files/
AFFYANNOTATORPATH := /Users/anikneja/Documents/bgee/extra/pipeline/curation/Affymetrix/
# Cel file path
CELPATH := $(AFFYDATAPATH)cel_data/
CELNEWPATH := $(AFFYNEWDATAPATH)cel_data/
CELANNPATH := $(AFFYANNOTATORPATH)cel_data/
# MAS5 file path
MAS5PATH := $(AFFYDATAPATH)processed_mas5/
MAS5NEWPATH := $(AFFYNEWDATAPATH)processed_mas5/
MAS5ANNPATH := $(AFFYANNOTATORPATH)processed_mas5/
# MAS5 original file path
MAS5ORIPATH := $(AFFYDATAPATH)processed_mas5_original_files/
MAS5ORINEWPATH := $(AFFYNEWDATAPATH)processed_mas5_original_files/
MAS5ORIANNPATH := $(AFFYANNOTATORPATH)processed_mas5_original_files/
# SCHUSTER file path
SCHUSTERPATH := $(AFFYDATAPATH)processed_schuster/
# Differential file path
DIFFEXPRPATH := $(AFFYDATAPATH)processed_differential/
# Bioconductor file path
BIOCONDUCTOR := $(AFFYDATAPATH)bioconductor/
BIOCONDUCTOROUT := $(BIOCONDUCTOR)out/
BIOCONDUCTORAFFIN := $(BIOCONDUCTOR)affinities/
BIOCONDUCTORDIFF := $(BIOCONDUCTOR)differential/
BIOCONDUCTORTARG := $(BIOCONDUCTOR)targets/
# Annotation file path
ANNOTATIONPATH := $(AFFYDATAPATH)annotations/
# Probsets to genes mapping file
PROBSETMAPPINGDIR := $(GENERATED_FILES_DIR)$(AFFYPATH)biomart
# =========== RNA_Seq FILES ===============
RNASEQPATH := RNA_Seq/
EXTRAMAPPING_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)mapToUberon.tsv
RNASEQ_EXPERIMENT_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqExperiment.tsv
RNASEQ_EXPERIMENT_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqExperiment_worm.tsv
RNASEQ_EXPERIMENT_FILEPATH_FULL := $(GENERATED_FILES_DIR)$(RNASEQPATH)RNASeqExperiment_full.tsv
RNASEQ_LIB_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqLibrary.tsv
RNASEQ_LIB_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqLibrary_worm.tsv
RNASEQ_LIB_FILEPATH_FULL := $(GENERATED_FILES_DIR)$(RNASEQPATH)RNASeqLibrary_full.tsv
RNASEQ_LIB_EXCLUSION_FILEPATH_WORM := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqLibrary_worm_exclusion.tsv
RNASEQ_LIB_CHECKS_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)RNASeqLibraryPlatformChecks.tsv
RNASEQ_SAMPINFO_FILEPATH := $(GENERATED_FILES_DIR)$(RNASEQPATH)rna_seq_sample_info.txt
RNASEQ_SAMPEXCLUDED_FILEPATH := $(GENERATED_FILES_DIR)$(RNASEQPATH)rna_seq_sample_excluded.txt
RNASEQ_BIOTYPE_EXCLUDED_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)biotypes_excluded_absent_calls.tsv
RNASEQ_LENGTH_INFO_FILEPATH := $(GENERATED_FILES_DIR)$(RNASEQPATH)rna_seq_length_info.txt
RNASEQ_ALREADY_DOWNLOADED := $(GENERATED_FILES_DIR)$(RNASEQPATH)rna_seq_sample_downloaded.txt
RNASEQ_GLOBIN_FILEPATH := $(SOURCE_FILES_DIR)$(RNASEQPATH)globin_info_per_species.tsv
RNASEQ_BGEECALL_FILE := $(GENERATED_FILES_DIR)$(RNASEQPATH)bgeecall_input.tsv
# RNAseq cluster paths
# TODO clean-up and remove unused ones
RNASEQ_DOWNLOAD_LIB_DIR := $(CLUSTER_CURNAGL_PATH)/downloads/
RNASEQ_DOWNLOAD_LIB_DIR_FASTQ := $(RNASEQ_DOWNLOAD_LIB_DIR)/FASTQ/RNAseq/
RNASEQ_CLUSTER_READONLY := $(CLUSTER_DATA_PATH)/
RNASEQ_CLUSTER_SCRIPTS := $(RNASEQ_CLUSTER_READONLY)GIT/pipeline/
RNASEQ_DOWNLOAD_GTF := $(RNASEQ_DOWNLOAD_LIB_DIR)GTF_$(MAJOR_RELEASE)/
RNASEQ_CLUSTER_GTF := $(RNASEQ_CLUSTER_READONLY)rna_seq/GTF_$(MAJOR_RELEASE)/
RNASEQ_CLUSTER_ALL_RES_BACKUP := $(RNASEQ_CLUSTER_READONLY)rna_seq/all_results_$(DBNAME)/
RNASEQ_CLUSTER_SCRATCH := $(CLUSTER_SCRATCH_RESULTS)rna_seq/
RNASEQ_CLUSTER_ABUNDANCE_ALL := $(RNASEQ_CLUSTER_SCRATCH)abundance_all_intergenic_$(DBNAME)/
RNASEQ_CLUSTER_SUM_RES := $(RNASEQ_CLUSTER_SCRATCH)sum_by_species_$(MAJOR_RELEASE)/
RNASEQ_CLUSTER_GAUSSIAN_CHOICE := $(OUTPUT_DIR)gaussian_choice_by_species.txt
RNASEQ_CLUSTER_PRESENCE_RES := $(RNASEQ_CLUSTER_SCRATCH)presence_absence_$(DBNAME)/
RNASEQ_CLUSTER_LOG := $(RNASEQ_CLUSTER_ABUNDANCE_ALL)
RNASEQ_CLUSTER_R_LOG := $(RNASEQ_CLUSTER_SCRATCH)Rout/
RNASEQ_CLUSTER_SBATCH := $(RNASEQ_CLUSTER_SCRATCH)sbatch/
RNASEQ_CLUSTER_REPORT_ALL := $(RNASEQ_CLUSTER_ABUNDANCE_ALL)reports_info_all_samples.txt
RNASEQ_CLUSTER_BGEECALL_OUTPUT := $(RNASEQ_CLUSTER_SCRATCH)calls/
RNASEQ_CLUSTER_BGEECALL_CALLS := $(RNASEQ_CLUSTER_BGEECALL_OUTPUT)all_results/
RNASEQ_CLUSTER_CALLS_STATS := $(RNASEQ_CLUSTER_BGEECALL_CALLS)presence_absence_all_samples.txt
RNASEQ_CLUSTER_KALLISTO_STATS := $(RNASEQ_CLUSTER_BGEECALL_CALLS)reports_info_all_samples.txt
ENCRYPT_PASSWD_FILE := $(RNASEQ_CLUSTER_READONLY).passw
# RNAseq sensitive cluster path
RNASEQ_SENSITIVE_FASTQ := $(RNASEQ_CLUSTER_READONLY)FASTQ/RNAseq/
# Intergenic folders
CLUSTER_REF_INTERGENIC_FOLDER := $(RNASEQ_CLUSTER_SCRATCH)ref_intergenic_$(MAJOR_RELEASE)/
CLUSTER_OTHER_INTERGENIC_FOLDER := $(RNASEQ_CLUSTER_SCRATCH)other_intergenic_$(MAJOR_RELEASE)/
# RNAseq kallisto index kmer size
RNASEQ_KALLISTO_KMER_DEFAULT := 31
RNASEQ_KALLISTO_KMER_SHORT := 15
# Max proportion of Ns allowed in intergenic sequences
INTERGENIC_N_PROPORTION := 0.05
# RNAseq data path
RNASEQDATAPATH := $(TMPDIR)/RNA_Seq/
ABUNDANCEFILE := gene_level_abundance+calls.tsv
RNASEQALLRES := $(RNASEQDATAPATH)rna_seq_all_results_$(DBNAME)/
SC_RNASEQ_ALL_RES_FL := $(RNASEQDATAPATH)full_length_all_results_$(DBNAME)/
RNASEQLOGS := $(RNASEQALLRES)
RNASEQSAMPSTATS := $(GENERATED_FILES_DIR)$(RNASEQPATH)presence_absence_all_samples.txt
RNASEQREPORTINFO := $(GENERATED_FILES_DIR)$(RNASEQPATH)reports_info_all_samples.txt
# Differential file path
#RNASEQDIFFEXPRPATH := $(RNASEQDATAPATH)processed_differential_$(DBNAME)/
#RNASEQDIFFEXPRPATH_DEVANDANAT := $(RNASEQDIFFEXPRPATH)devAndAnat/
#RNASEQDIFFEXPRPATH_SEX := $(RNASEQDIFFEXPRPATH)sex/
# Bioconductor file path
RNASEQBIOCONDUCTOR := $(RNASEQDATAPATH)bioconductor_$(DBNAME)/
#XXX is it used anymore???
#RNASEQBIOCONDUCTORDIFF := $(RNASEQBIOCONDUCTOR)differential/
#RNASEQBIOCONDUCTORTARG := $(RNASEQBIOCONDUCTOR)targets/
#RNASEQBIOCONDUCTORTARG_SEX := $(RNASEQBIOCONDUCTORTARG)sex/
#RNASEQBIOCONDUCTORTARG_DEVANDANAT := $(RNASEQBIOCONDUCTORTARG)devAndAnat/
# TMM normalization files
RNASEQTMMTARG := $(RNASEQBIOCONDUCTOR)targets_TMM/
RNASEQTMMPATH := $(RNASEQDATAPATH)processed_TMM_$(DBNAME)/
# =========== SINGLE CELL RNA_Seq FILES ===============
# scRNASeq github file paths in the source directory
SC_RNASEQ_PATH := scRNA_Seq/
SC_RNASEQ_PATH_SOURCE := $(SOURCE_FILES_DIR)$(SC_RNASEQ_PATH)
SC_RNASEQ_ACCEPTED_PROTOCOLS := $(SC_RNASEQ_PATH_SOURCE)acceptedProtocols.tsv
### Full_length
SC_RNASEQ_FL_FOLDER_SOURCE := $(SC_RNASEQ_PATH_SOURCE)Full_length/
# FL and TB annotations are in the same file. Kept FL and TB annotation in different directories in case only one out of the two single cell pipeline is run for a release of Bgee
SC_RNASEQ_LIB_FL_FILEPATH := $(SC_RNASEQ_FL_FOLDER_SOURCE)scRNASeqLibrary_merged.tsv
SC_RNASEQ_EXP_FL_FILEPATH := $(SC_RNASEQ_FL_FOLDER_SOURCE)scRNASeqExperiment.tsv
### Target_based
SC_RNASEQ_TB_FOLDER_SOURCE := $(SC_RNASEQ_PATH_SOURCE)Target_based/
# FL and TB annotations are in the same file. Kept FL and TB annotation in different directories in case only one out of the two single cell pipeline is run for a release of Bgee
SC_RNASEQ_LIB_TB_FILEPATH := $(SC_RNASEQ_TB_FOLDER_SOURCE)scRNASeqLibrary_merged.tsv
SC_RNASEQ_EXP_TB_FILEPATH := $(SC_RNASEQ_TB_FOLDER_SOURCE)scRNASeqExperiment.tsv
SC_RNASEQ_MANIFEST_FILE_FILEPATH := $(SC_RNASEQ_TB_FOLDER_SOURCE)Manifest_file.tsv
SC_RNASEQ_WHITELIST_10X_v2 := $(SC_RNASEQ_TB_FOLDER_SOURCE)barcode_whitelist_10X_v2.txt.zip
SC_RNASEQ_WHITELIST_10X_v3 := $(SC_RNASEQ_TB_FOLDER_SOURCE)barcode_whitelist_10X_v3.txt.zip
# scRNASeq github file paths in the generated_files directory
SC_RNASEQ_PATH_GENERATED := $(GENERATED_FILES_DIR)$(SC_RNASEQ_PATH)
SC_RNASEQ_DOWNLOADED_LIB_FILEPATH := $(SC_RNASEQ_PATH_GENERATED)librariesDownloaded.tsv
### Full_length
SC_RNASEQ_FL_FOLDER_GENERATED := $(SC_RNASEQ_PATH_GENERATED)Full_length/
SC_RNASEQ_LIB_PASS_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)passScRNASeqLibrary.tsv
SC_RNASEQ_LIB_NOT_PASS_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)notPassScRNASeqLibrary.tsv
SC_RNASEQ_METADATA_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)metadata_info.tsv
SC_RNASEQ_METADATA_NOT_MATCH_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)metadata_info_not_match.tsv
SC_RNASEQ_SAMPINFO_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)scrna_seq_sample_info.tsv
SC_RNASEQ_SAMPINFO_PASS_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)NEW_scRNASeq_sample_info.tsv
SC_RNASEQ_SAMPINFO_NOT_PASS_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)Discard_scRNASeq_sample_info.tsv
SC_RNASEQ_MODALITY_FILEPATH := $(SC_RNASEQ_FL_FOLDER_GENERATED)Modality_Cell_type_per_experiment.tsv
SC_RNASEQ_BGEECALL_FILE_FULL_LENGTH := $(SC_RNASEQ_FL_FOLDER_GENERATED)bgeecall_input.tsv
SC_RNASEQ_SAMP_STATS_FL := $(SC_RNASEQ_FL_FOLDER_GENERATED)presence_absence_all_samples.txt
SC_RNASEQ_REPORT_INFO_FL := $(SC_RNASEQ_FL_FOLDER_GENERATED)reports_info_all_samples.txt
### Target_based
SC_RNASEQ_TB_FOLDER_GENERATED := $(SC_RNASEQ_PATH_GENERATED)Target_based/
SC_RNASEQ_TB_DOWNLOADED_LIB_FILEPATH := $(SC_RNASEQ_TB_FOLDER_GENERATED)librariesDownloaded.tsv
SC_RNASEQ_EXP_TB_FILEPATH_FILTERED := $(SC_RNASEQ_TB_FOLDER_GENERATED)scRNASeqExperiment.tsv
SC_RNASEQ_LIB_TB_FILEPATH_FILTERED := $(SC_RNASEQ_TB_FOLDER_GENERATED)scRNASeqLibrary_merged.tsv
SC_RNASEQ_CLEANED_BARCODES := $(SC_RNASEQ_TB_FOLDER_GENERATED)cleaned_barcodes/
SC_RNASEQ_METADATA_10X_FILEPATH := $(SC_RNASEQ_TB_FOLDER_GENERATED)metadata_info_10X.txt
SC_RNASEQ_METADATA_10X_NOT_MATCH_FILEPATH := $(SC_RNASEQ_TB_FOLDER_GENERATED)metadata_notMatch_10X.txt
SC_RNASEQ_SAMPINFO_10X_FILEPATH := $(SC_RNASEQ_PATH_GENERATED)scRNA_Seq_info_TargetBased.txt
SC_RNASEQ_REPORT_INFO_TB := $(SC_RNASEQ_FL_FOLDER_GENERATED)reports_info_all_samples.txt
# scRNAseq cluster paths (CURNAGL)
SC_RNASEQ_DOWNLOAD_PATH := $(CLUSTER_CURNAGL_PATH)/downloads/
SC_RNASEQ_DOWNLOAD_PATH_LIB_DIR := $(SC_RNASEQ_DOWNLOAD_PATH)scRNA_Seq_All/
SC_RNASEQ_DOWNLOAD_PATH_FULL_LENGTH := $(SC_RNASEQ_DOWNLOAD_PATH_LIB_DIR)scRNASeq_libraries_FullLength/
SC_RNASEQ_DOWNLOAD_PATH_DROPLET := $(SC_RNASEQ_DOWNLOAD_PATH_LIB_DIR)scRNASeq_libraries_Droplet_10X/
# scRNAseq cluster sofware
SCRNASEQ_SOFTWARE_BAMTOFASTQ := /users/jwollbre/tools/bamtofastq_linux
# scRNAseq cluster paths (SENSITIVE)
## PATH to full length and 10X data
SC_RNASEQ_FASTQ_FULL_LENGTH := $(CLUSTER_DATA_PATH)/FASTQ/scRNAseq/Full_length/
SC_RNASEQ_FASTQ_DROPLET := $(CLUSTER_DATA_PATH)/FASTQ/scRNAseq/10X/
## PATH to all results of both of pipelines
SC_RNASEQ_CLUSTER_ALL_RES := $(CLUSTER_DATA_PATH)/$(DBNAME)/scRNA-Seq_all_results/
## Specific paths to results of full-length protocols
SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH := $(SC_RNASEQ_CLUSTER_ALL_RES)FULL_LENGTH/
SC_RNASEQ_CLUSTER_BGEECALL := $(SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH)BgeeCall/
SC_RNASEQ_FL_CLUSTER_R_LOG := $(SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH)Rout/
SC_RNASEQ_CLUSTER_KALLISTO := $(SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH)Kallisto_All_Cells/
SC_RNASEQ_CLUSTER_QC_CELLPOP_RES := $(SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH)Quality_Control_Cell_Population/
SC_RNASEQ_CLUSTER_CALL_PRESENT := $(SC_RNASEQ_CLUSTER_ALL_RES_FULL_LENGTH)scRNAseq_Callpresent/
# scRNASeq file paths
SC_RNASEQ_MODALITY_CELL_POP := $(SC_RNASEQ_CLUSTER_QC_CELLPOP_RES)Modality_Cell_type_per_experiment.tsv
SC_RNASEQ_CLUSTER_CALLS_STATS := $(SC_RNASEQ_CLUSTER_BGEECALL)presence_absence_all_samples.txt
SC_RNASEQ_CLUSTER_KALLISTO_STATS := $(SC_RNASEQ_CLUSTER_BGEECALL)reports_info_all_samples.txt
## Specific paths to results of target-based protocols
SC_RNASEQ_STATS_LIBRARIES_10X := $(SC_RNASEQ_TB_FOLDER_GENERATED)/stats_libraries.txt
## on sensitive cluster
SC_RNASEQ_CLUSTER_ALL_RES_DROPLET := $(SC_RNASEQ_CLUSTER_ALL_RES)DROPLET_10X/
SC_RNASEQ_CLUSTER_RES_KALLISTO_DROPLET := $(SC_RNASEQ_CLUSTER_ALL_RES_DROPLET)kallisto_bus_results/
SC_RNASEQ_CLUSTER_QC_CELLTYPE := $(SC_RNASEQ_CLUSTER_ALL_RES_DROPLET)QC_CellType_identification/
# scRNASeq file paths
SC_RNASEQ_INFO_ALL_LIBRARIES_10X := $(SC_RNASEQ_CLUSTER_QC_CELLTYPE)InformationAllLibraries.txt
SC_RNASEQ_CLUSTER_CALLS_10X := $(SC_RNASEQ_CLUSTER_ALL_RES_DROPLET)calls/
SC_RNASEQ_CLUSTER_INFO_CALLS_10X := $(SC_RNASEQ_CLUSTER_CALLS_10X)All_cellPopulation_stats_10X.tsv
## On Bgee server
SC_RNASEQ_SERVER_RES_KALLISTO_DROPLET := $(TMPDIR)/DROPLET_10X/kallisto_bus_results/
SC_RNASEQ_SERVER_CALLS_10X := $(TMPDIR)/DROPLET_10X/calls/
SC_RNASEQ_SERVER_INFO_CALLS_10X := $(SC_RNASEQ_SERVER_CALLS_10X)All_cellPopulation_stats_10X.tsv
# minimum number of cells in a full-length library
MIN_CELLS_PER_LIBRARY_FULL_LENGTH := 50
# p-value used as cutoff
PVALUE_CUTOFF := 0.05
# =========== DOWNLOAD FILES ===============
# path to the root of the directory to use to store generated download files
DOWNLOAD_FILE_ROOT_PATH := $(TMPDIR)/download_files/
XREFS_PATH := $(TMPDIR)/xrefs/
EASYBGEE_PATH := $(TMPDIR)/$(DBNAME_EASYBGEE)/
R_SPECIES_INFO := $(TMPDIR)/rPackageSpeciesInfo.tsv
# paths of the different file types, relative to DOWNLOAD_FILE_ROOT_PATH
CALLS_PATH := calls/expr_calls/
H5AD_PATH := h5ad/
EXPR_CALLS_PATH := $(CALLS_PATH)expr_calls/
DIFF_EXPR_CALLS_PATH := $(CALLS_PATH)diff_expr_calls/
PROC_EXPR_VALUES_PATH := processed_expr_values/
ORTHOLOGS_PATH := orthologs/
MULTI_SPE_DIFF_EXPR_CALL_PATH := $(CALLS_PATH)multi_species_diff_expr_calls/
EXPR_VALUES_PATH := processed_expr_values/
RNA_SEQ_EXPR_VALUES_PATH := $(EXPR_VALUES_PATH)rna_seq/
AFFYMETRIX_EXPR_VALUES_PATH := $(EXPR_VALUES_PATH)affymetrix/
# file suffixes
EXPR_SIMPLE_SUF := _expr_simple.tsv
EXPR_SIMPLE_DEV_SUF := _expr_simple_development.tsv
EXPR_COMPLETE_SUF := _expr_advanced.tsv
EXPR_COMPLETE_DEV_SUF := _expr_advanced_development.tsv
DIFF_EXPR_ANATOMY_SIMPLE_SUF := _diffexpr-anatomy-simple.tsv
DIFF_EXPR_ANATOMY_COMPLETE_SUF := _diffexpr-anatomy-complete.tsv
DIFF_EXPR_DEV_SIMPLE_SUF := _diffexpr-development-simple.tsv
DIFF_EXPR_DEV_COMPLETE_SUF := _diffexpr-development-complete.tsv
ORTHOLOGS_SUF := _orthologs.tsv
MULTI_SPE_DIFF_EXPR_ANATOMY_SIMPLE_SUF := _multi-diffexpr-anatomy-simple.tsv
MULTI_SPE_DIFF_EXPR_ANATOMY_COMPLETE_SUF := _multi-diffexpr-anatomy-complete.tsv
RNA_SEQ_EXP_LIB_SUF_ZIP := _RNA-Seq_experiments_libraries.zip
RNA_SEQ_COUNT_SUF_ZIP := _RNA-Seq_read_counts_TPM_FPKM.zip
AFFYMETRIX_EXP_CHIP_SUF_ZIP := _Affymetrix_experiments_chips.zip
AFFYMETRIX_PROBESET_SUF_ZIP := _Affymetrix_probesets.zip
# FTP informations
FTP_URL := bgeeftp.unil.ch
FTP_ROOT := /u01/ftp/
FTP_CURRENT := $(FTP_ROOT)$(DBNAME)/
FTP_DOWNLOAD := $(FTP_CURRENT)download/
# =========== RANK DOWNLOAD FILES ===============
# Directories related to $(OUTPUT_DIR)
RANKS_PER_ANAT := ranks/anat_entity/
RANKS_PER_CONDITION := ranks/condition/
# =========== TRIPLE STORE FILES ===============
ONTOP_BGEE_PROP_TEMPLATE := $(INPUT_DIR)bgee_connection.template
GENEX_ONTOLOGY_URL := https://raw.githubusercontent.com/biosoda/genex/master/genex_reduced_subsumption.ttl
ONTOP_DOWNLOAD_URL := https://netcologne.dl.sourceforge.net/project/ontop4obda/ontop-5.1.0/ontop-cli-5.1.0.zip
ONTOP_MYSQL_JDBC_URL := https://repo1.maven.org/maven2/mysql/mysql-connector-java/5.1.48/mysql-connector-java-5.1.48.jar
GENEX_MAPPING_URL := https://raw.githubusercontent.com/biosoda/bioquery/master/Bgee_OBDA_mappings/bgee_v15_1_genex.obda
ONTOP_DOWNLOAD_FILE := ontop.zip
GENEX_ONTOLOGY_FILE := genex.owl
GENEX_MAPPING_FILE := bgee_genex.obda
ONTOP_INSTALL_DIR := /usr/local/ontop/
ISQL_PATH := /usr/local/virtuoso-open-source/bin/isql
VIRTUOSO_HOST := localhost:1111
TTL_DIRECTORY_FULL_PATH := $(OUTPUT_DIR)
FTP_SAVE_DUMP_PATH := $(FTP_CURRENT)rdf_easybgee.zip
TTL_FILE_LIST := $(TTL_DIRECTORY_FULL_PATH)ttl_files.txt
BGEE_VIRTUOSO_FILE := $(TTL_DIRECTORY_FULL_PATH)add_bgee_virtuoso.sql
ZIP_TTL_FILE := $(TTL_DIRECTORY_FULL_PATH)rdf_easybgee.zip