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config.mk
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############################## HEADER ##########################################
#
# This is a template of a configuration file.
#
################################################################################
############################## INFRASTRUCTURE ##################################
# This section must contain only general infrastructure variables.
# NOTE: Varable names can end with '_d', '_f', '_r', '_t' and '_l'.
# They represent, respectively, directories, files, references, temporaries and
# lists values inside them.
# Only names ending with '_l' can have non-single string values, but you can
# compose'em: OUTPUTS_dlt (for a list of temporary directories).
# There could be an user for the container (ex. lion).
# So, C_BASE_d must be set accordingly:
DEFAULT_USER := $(if $(SWITCH),lion,)
POCKET := $(if $(prefix),$(prefix),$(PWD))
# Host's base directory, outside the container: $(PWD).
H_BASE_d := $(abspath $(POCKET))
H_CONFIG_d := $(H_BASE_d)/config
H_INPUTS_d := $(H_BASE_d)/inputs
H_OUTPUTS_d := $(H_BASE_d)/outputs
H_ASSETS_d := $(H_BASE_d)/assets
H_REFERENCE_d := $(H_BASE_d)/reference
H_ANNOTATION_d := $(H_BASE_d)/annotation
H_EXTRA_d := $(H_BASE_d)/extra
H_TMP_d := $(H_BASE_d)/tmp
# Container's base directory: /home.
C_BASE_d := /home/$(DEFAULT_USER)
C_CONFIG_d := $(C_BASE_d)/config
C_INPUTS_d := $(C_BASE_d)/inputs
C_OUTPUTS_d := $(C_BASE_d)/outputs
C_ASSETS_d := $(C_BASE_d)/assets
C_REFERENCE_d := $(C_BASE_d)/reference
C_ANNOTATION_d := $(C_BASE_d)/annotation
C_EXTRA_d := $(C_BASE_d)/extra
C_TMP_d := $(C_BASE_d)/tmp
# Mount some important files in their respective folders. Must use ionly absolute paths!
MP_CONFIG_l := $(PWD)/Makefile $(PWD)/config.mk
MP_INPUTS_l := $(H_INPUTS_d)/ponga.txt
MP_OUTPUTS_l :=
MP_ASSETS_l := /home/scratch60/lbuzzo/RTC/neopipe/assets/ref.perldb
MP_REFERENCE_l := /home/genomes/Homo_sapiens/hg38/hg38.fa
MP_ANNOTATION_l := /home/projects2/databases/gencode/release29/gencode.v29.annotation.gff3.gz
MP_EXTRA_l :=
MP_TMP_l :=
############################## APP SPECIFIC VARIABLES ##########################
# This section must contain variables specific to the application.
# General pipeline data: name and file suffixes.
PIPELINE := CUSTOM
SUFFIXES :=
# Meta-targets.
TARGET3 :=
TARGET3_REQUISITES :=
TARGET3_RECIPES :=
TARGET2 :=
TARGET2_REQUISITES :=
TARGET2_RECIPES :=
TARGET1 :=
TARGET1_REQUISITES :=
TARGET1_RECIPES :=
TARGET0 :=
TARGET0_REQUISITES :=
TARGET0_RECIPES :=