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Meltfile
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Meltfile
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#!/usr/bin/env make
############################## HEADER ##########################################
#
# Makefile for sandy stuff...
#
################################################################################
# Default system path at runtime: prefix.
PFX := $(if $(prefix),$(abspath $(strip $(wildcard $(prefix)))),)
override prefix := $(if $(prefix),$(if $(PFX),$(PFX),ERROR),$(CURDIR))
ifeq ($(prefix),ERROR)
$(error "Invalid value for prefix variable")
endif
# Environment determination (container or host).
SWITCH_HAS := [ -f "/.dockerenv" ] && echo "1"
SWITCH := $(if $(shell $(SWITCH_HAS)),1,)
############################## APP SPECIFICS ###################################
# App specific runtime data: constants.
H_ROOT_DIR := /home/users/jlbuzzo/projects_old/MELT2docker
C_ROOT_DIR := /build
ROOT_DIR := $(if $(SWITCH),$(C_ROOT_DIR),$(H_ROOT_DIR))
RUNNING_DIR := $(CURDIR)
APP := MELT2docker
VERSION := 0.1
ID := npp_123456
KEY := $(ROOT_DIR)/keys/key.pub
LICENSE := $(ROOT_DIR)/LICENSE
MANUAL := $(ROOT_DIR)/doc/neopipe.pod
SITE := https://galantelab.github.io/neopipe
REPO := https://github.com/galantelab/neopipe
CLOUD := https://www.aws.com/galantelab/neopipe
CONFIGFILE :=
ENCAPSULATE :=
CLOUDERIZE :=
CLOUDFILE := $(RUNNING_DIR)/aws.yml
DOCKERIZE :=
DOCKERFILE := $(RUNNING_DIR)/docker/Dockerfile
IMAGE := galantelab/MELT2docker
MAKERIZE :=
MAKEFILE := $(RUNNING_DIR)/Makefile
TARBALL := $(RUNNING_DIR)/$(APP)-master.tar.gz
# Main command.
CMD :=
# List of important files. Mount them in their respective folders.
# Must use only absolute paths!
MP_CONFIG_l :=
MP_INPUTS_l :=
MP_OUTPUTS_l :=
MP_ASSETS_l :=
MP_REFERENCE_l :=
MP_ANNOTATION_l :=
MP_EXTRA_l :=
MP_TMP_l :=
# Some important input files.
MELT_PLACE := $(ROOT_DIR)/deps/MELTv2.1.4
MEI_PLACE := $(MELT_PLACE)/me_refs/Hg38
HERVK_ZIP := $(MEI_PLACE)/HERVK_MELT.zip
LINE1_ZIP := $(MEI_PLACE)/LINE1_MELT.zip
ALU_ZIP := $(MEI_PLACE)/ALU_MELT.zip
SVA_ZIP := $(MEI_PLACE)/SVA_MELT.zip
# Some commands.
JAR := $(MELT_PLACE)/MELT.jar
PREPROCESS := java -Xmx2G -jar $(JAR) Preprocess
INDIV_ANALYSIS := java -Xmx4G -jar $(JAR) IndivAnalysis
GROUP_ANALYSIS := java -Xmx6G -jar $(JAR) GroupAnalysis
GENOTYPE := java -Xmx2G -jar $(JAR) Genotype
MAKE_VCF := java -Xmx2G -jar $(JAR) MakeVCF
CALU := java -Xmx2G -jar $(JAR) CALU
LINEU := java -Xmx2G -jar $(JAR) LINEU
# Dicovery directories for each result.
BASE_DISCOVERY_d := $(OUTPUTS_d)/results
HERVK_DISCOVERY_d := $(BASE_DISCOVERY_d)/HERVK
LINE1_DISCOVERY_d := $(BASE_DISCOVERY_d)/LINE1
ALU_DISCOVERY_d := $(BASE_DISCOVERY_d)/ALU
SVA_DISCOVERY_d := $(BASE_DISCOVERY_d)/SVA
############################## MISCELLANEOUS ###################################
# This section must contain some common variables, like reference genomes and
# annotations files.
# Reference files and annotations.
REFERENCE_GENOME := $(MP_REFERENCE_l)
REFERENCE_GTF := $(MP_ANNOTATION_l)
REFERENCE_BED := $(MELT_PLACE)/add_bed_files/Hg38/Hg38.genes.bed
REP_ANNOTATION := $(ANNOTATION_d)/rep.hg38.converted.bed
REP_ANNOTATION_manual := $(ANNOTATION_d)/rep.hg38.converted.manual.bed
BAM_COVERAGE := 40
############################## OVERRIDE CONFIGURATIONS #########################
# Default configuration file.
DFT_CONFIG := $(abspath $(strip $(wildcard $(RUNNING_DIR)/config.mk)))
# User defined configuration file.
CFG := $(if $(CONFIGFILE),$(abspath $(strip $(wildcard $(CONFIGFILE)))),)
CONFIG_f := $(if $(CONFIGFILE),$(if $(CFG),$(CFG),ERROR),$(DFT_CONFIG))
# Launch an error if a nonexistent configuration file was defined by the user.
ifeq ($(CONFIG_f),ERROR)
$(error Configuration file \"$(CONFIGFILE)\" doesn\'t exist)
endif
# Include configuration file, if exists.
ifeq ($(CONFIG_f),)
$(warning Warning: No configuration file specified. Using defaults.)
else
include $(CONFIG_f)
endif
############################## PREAMBLE ########################################
# General module info and macros.
# --- Common command macros.
USER := $(shell whoami)
DATE := $(shell date --utc)
SHELL := bash
ECHO := echo -e
MKDIR := mkdir -p
PING := ping -c1
RM := rm -rf
CC := gcc
CFLAGS :=
# --- Common color macros.
GREEN := "\033[0;32m"
YELLOW := "\033[0;33m"
RED := "\033[0;31m"
WINE := "\033[0;35m"
RESET := "\033[0;m"
# Autotools default paths here.
############################## 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).
DEFAULT_USER := lion
# Host's base directory, outside the container: $(prefix).
H_BASE_d := $(prefix)
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 := $(C_BASE_d)/tmp
############################## CONDITIONALS ####################################
# A common internal representation for paths, based on ENCAPSULATE.
ifeq ($(ENCAPSULATE),yes)
BASE_d := $(if $(SWITCH),$(C_BASE_d),$(H_BASE_d))
CONFIG_d := $(if $(SWITCH),$(C_CONFIG_d),$(H_CONFIG_d))
INPUTS_d := $(if $(SWITCH),$(C_INPUTS_d),$(H_INPUTS_d))
OUTPUTS_d := $(if $(SWITCH),$(C_OUTPUTS_d),$(H_OUTPUTS_d))
ASSETS_d := $(if $(SWITCH),$(C_ASSETS_d),$(H_ASSETS_d))
REFERENCE_d := $(if $(SWITCH),$(C_REFERENCE_d),$(H_REFERENCE_d))
ANNOTATION_d := $(if $(SWITCH),$(C_ANNOTATION_d),$(H_ANNOTATION_d))
EXTRA_d := $(if $(SWITCH),$(C_EXTRA_d),$(H_EXTRA_d))
TMP_d := $(if $(SWITCH),$(C_TMP_d),$(H_TMP_d))
INFRASTRUCTURE_dl := $(CONFIG_d) $(INPUTS_d) $(OUTPUTS_d) $(ASSETS_d)
INFRASTRUCTURE_dl += $(REFERENCE_d) $(ANNOTATION_d) $(EXTRA_d) $(TMP_d)
INFRASTRUCTURE_sl := CONFIG_d INPUTS_d OUTPUTS_d ASSETS_d
INFRASTRUCTURE_sl += REFERENCE_d ANNOTATION_d EXTRA_d TMP_d
MAPPINGS_fl := $(MP_CONFIG_l) $(MP_INPUTS_l) $(MP_OUTPUTS_l) $(MP_ASSETS_l)
MAPPINGS_fl += $(MP_REFERENCE_l) $(MP_ANNOTATION_l) $(MP_EXTRA_l) $(MP_TMP_l)
MAPPINGS_sl := MP_CONFIG_l MP_INPUTS_l MP_OUTPUTS_l MP_ASSETS_l
MAPPINGS_sl += MP_REFERENCE_l MP_ANNOTATION_l MP_EXTRA_l MP_TMP_l
else
BASE_d := $(if $(SWITCH),$(C_BASE_d),$(H_BASE_d))
CONFIG_d := $(BASE_d)
INPUTS_d := $(BASE_d)
OUTPUTS_d := $(BASE_d)
ASSETS_d := $(BASE_d)
REFERENCE_d := $(BASE_d)
ANNOTATION_d := $(BASE_d)
EXTRA_d := $(BASE_d)
TMP_d := $(BASE_d)
INFRASTRUCTURE_dl := $(BASE_d)
INFRASTRUCTURE_sl := BASE_d
MAPPINGS_fl := $(MP_CONFIG_l) $(MP_INPUTS_l) $(MP_OUTPUTS_l) $(MP_ASSETS_l)
MAPPINGS_fl += $(MP_REFERENCE_l) $(MP_ANNOTATION_l) $(MP_EXTRA_l) $(MP_TMP_l)
MAPPINGS_sl := MP_CONFIG_l MP_INPUTS_l MP_OUTPUTS_l MP_ASSETS_l
MAPPINGS_sl += MP_REFERENCE_l MP_ANNOTATION_l MP_EXTRA_l MP_TMP_l
endif
# --- Support programs data.
# Upipe management info (works only on Linux).
UPIPE_SITE := https://galantelab.github.io/upipe/
UPIPE_REPO := https://github.com/jlbuzzo/upipe.git
UPIPE_TARBALL := https://github.com/jlbuzzo/upipe/archive/master.tar.gz
UPIPE_BUILD := $(build)/upipe-$(basename $(basename $(notdir $(UPIPE_TARBALL))))
UPIPE_PATH := ~/bin
UPIPE_IMAGE := galantelab/upipe:latest
# Git management info (works only on linux).
GIT_SITE := https://git-scm.com/
GIT_REPO := https://github.com/git/git.git
GIT_TARBALL := https://github.com/git/git/archive/master.tar.gz
GIT_TARBALL2 := https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.20.1.tar.gz
GIT_BUILD := $(build)/git-$(basename $(basename $(notdir $(GIT_TARBALL))))
GIT_BUILD2 := $(build)/$(basename $(basename $(notdir $(GIT_TARBALL2))))
GIT_PATH := /usr/bin
GIT_IMAGE :=
GIT_CLONE := git clone
# Docker management info (works only on Linux).
DOCKER_SITE := https://www.docker.com/
DOCKER_REPO := https://github.com/docker/docker.git
DOCKER_URL := https://github.com/docker/docker/archive/master.tar.gz
DOCKER_URL2 := https://download.docker.com/linux/static/stable/x86_64/docker-18.09.1.tgz
DOCKER_TARBALL := $(build)/$(notdir $(DOCKER_URL))
DOCKER_TARBALL2 := $(build)/$(notdir $(DOCKER_URL2))
DOCKER_BUILD := $(build)
DOCKER_PATH := /usr/bin
# --- General system tests.
INTERNET_HAS := read <<< "$$($(PING) www.google.com 2> /dev/null)" && echo -n $$REPLY
INTERNET_GET := $(if $(shell $(INTERNET_HAS)),,internet_configure)
CAPSULE_HAS := [ "$(ENCAPSULATE)" == "yes" ] && echo "1"
CAPSULE_GET := $(if $(shell $(CAPSULE_HAS)),capsule_mount,)
MAKE_HAS := [ -n "$$(which make)" ] && echo "1"
MAKE_GET := $(if $(shell $(MAKE_HAS)),,make_install)
GIT_HAS := [ -n "$$(which git)" ] && echo "1"
GIT_GET := $(if $(shell $(GIT_HAS)),,git_install)
DOCKER_HAS := [ -n "$$(which docker)" ] && echo "1"
DOCKER_GET := $(if $(shell $(DOCKER_HAS)),,docker_install)
PERL_HAS := [ -n "$$(which perl)" ] && echo "1"
PERL_GET := $(if $(shell $(PERL_HAS)),,perl_install)
CPAN_HAS := [ -n "$$(which cpan)" ] && echo "1"
CPAN_GET := $(if $(shell $(CPAN_HAS)),,cpan_install)
CPANM_HAS := [ -n "$$(which cpanm)" ] && echo "1"
CPANM_GET := $(if $(shell $(CPANM_HAS)),,cpanm_install)
PERLBREW_HAS := [ -n "$$(which perlbrew)" ] && echo "1"
PERLBREW_GET := $(if $(shell $(PERLBREW_HAS)),,perlbrew_install)
CONDA_HAS := [ -n "$$(which conda)" ] && echo "1"
CONDA_GET := $(if $(shell $(CONDA_HAS)),,conda_install)
UPIPE_HAS := [ -f "$(UPIPEFILE)" ] && echo "1"
UPIPE_GET := $(if $(shell $(UPIPE_HAS)),,upipe_install)
CLOUD_HAS := [ -n "$$(which aws)" ] && echo "1"
CLOUD_GET := $(if $(shell $(CLOUD_HAS)),,aws_install)
# Specific tests.
USE_MODE := $(if $(DOCKERIZE),app_docker_run,app_native_run)
DOCKERFILE_HAS := [ -f "$(DOCKERFILE)" ] && echo "1"
DOCKERFILE_GET := $(if $(shell $(DOCKERFILE_HAS)),,dockerfile_get)
IMAGE_GET_MODE := $(if $(shell $(DOCKERFILE_HAS)),image_build,image_pull)
IMAGE_HAS := echo -n "$$(sed -n '\|^$(IMAGE) |{p}' <<< "$$(docker images 2> /dev/null)")" | grep -w 'latest'
IMAGE_GET := $(if $(shell $(IMAGE_HAS)),,$(IMAGE_GET_MODE))
TARBALL_HAS := [ -f "$(TARBALL)" ] && echo "1"
TARBALL_GET := $(if $(shell $(TARBALL_HAS)),,repo)
APP_HAS := [ -n "$$(which $(APP))" ] && echo "1"
APP_HAS_MODE := $(if $(DOCKERIZE),$(IMAGE_HAS),$(APP_HAS))
APP_GET_MODE := $(if $(DOCKERIZE),$(IMAGE_GET),app_install)
APP_GET := $(if $(shell $(APP_HAS_MODE)),,$(APP_GET_MODE))
############################## APP SPECIFIC PRE-PROCCESSING ####################
# General pipeline's data files: suffixes.
SFX ?= .txt
INPUT ?= $(RUNNING_DIR)
# Validate INPUTS against emptyness.
INPUTS_PROCESSED := $(word 1, $(abspath $(strip $(wildcard $(MP_INPUTS_l)))))
$(if $(INPUTS_PROCESSED),, $(error No input candidates in $(INPUTS_d) folder))
# Search and validate INPUTS from a given string list, directory, or file, by
# the SUFFIXES list criteria.
#INPUTS_PROCESSED := $(shell $(SCRIPTS)/ufinder.sh $(INPUTS_PROCESSED) $(SUFFIXES))
# A limited alternative validation process (without 'ufinder' script).
INPUTS_PROCESSED := $(if $(shell [ -f "$(INPUTS_PROCESSED)" ] && echo "1"),$(filter %$(SFX), $(shell cat $(INPUTS_PROCESSED))),$(wildcard $(INPUTS_PROCESSED)/*$(SFX)))
INPUTS_PROCESSED := $(abspath $(strip $(wildcard $(INPUTS_PROCESSED))))
$(if $(INPUTS_PROCESSED),, $(error No valid $(SFX) file specified))
# ATTENTION: Variables that are string lists has an '_l' suffix appendedd to
# the end of their names. Their behavior differently in pattern rules.
# Folder for timestamps.
TMSTP_d := $(OUTPUTS_d)/tmstp
# Carrefully set the INPUTS_l variable after success validations.
INPUTS_l := $(INPUTS_PROCESSED)
INPUTS_FILENAME_l := $(strip $(notdir $(INPUTS_l)))
INPUTS_BASENAME_l := $(strip $(basename $(notdir $(INPUTS_l))))
INPUTS_dl := $(strip $(dir $(INPUTS_l)))
#INPUTS_BASENAME_dl :=
#OUTPUTS_l :=
#OUTPUTS_FILENAME_l :=
#OUTPUTS_BASENAME_l :=
#OUTPUTS_dl :=
OUTPUTS_BASENAME_dl := $(addprefix $(OUTPUTS_d)/, $(INPUTS_BASENAME_l))
OUTPUTS_l := $(strip $(join $(OUTPUTS_BASENAME_dl), $(addprefix /, $(INPUTS_FILENAME_l))))
#OUTPUTS_l := $(OUTPUTS_l:.bam=.sorted.bam)
# Derivated lists: '.bai', '.abnormal', '.disc', '.disc.bai' and others.
OUTPUTS_BAM_l := $(OUTPUTS_l)
OUTPUTS_BAI_l := $(addsuffix .bai, $(OUTPUTS_l))
OUTPUTS_ABNORMAL_l := $(addsuffix .abnormal, $(OUTPUTS_l))
OUTPUTS_DISC_l := $(addsuffix .disc, $(OUTPUTS_l))
OUTPUTS_DISC_BAI_l := $(addsuffix .disc.bai, $(OUTPUTS_l))
OUTPUTS_DISC_FQ_l := $(addsuffix .disc.fq, $(OUTPUTS_l))
# Timestamp lists, terminated in '_lt'.
# Lists for individual analysis.
OUTPUTS_HERVK_INDIV_lt := $(addsuffix .hervk.indiv.tmstp, $(OUTPUTS_l))
OUTPUTS_LINE1_INDIV_lt := $(addsuffix .line1.indiv.tmstp, $(OUTPUTS_l))
OUTPUTS_ALU_INDIV_lt := $(addsuffix .alu.indiv.tmstp, $(OUTPUTS_l))
OUTPUTS_SVA_INDIV_lt := $(addsuffix .sva.indiv.tmstp, $(OUTPUTS_l))
# Simple timestamps files for group analysis.
OUTPUTS_HERVK_GRP_t := $(TMSTP_d)/common.bam.hervk.group.tmstp
OUTPUTS_LINE1_GRP_t := $(TMSTP_d)/common.bam.line1.group.tmstp
OUTPUTS_ALU_GRP_t := $(TMSTP_d)/common.bam.alu.group.tmstp
OUTPUTS_SVA_GRP_t := $(TMSTP_d)/common.bam.sva.group.tmstp
# Lists for genotype analysis.
OUTPUTS_HERVK_GEN_lt := $(addsuffix .hervk.gen.tmstp, $(OUTPUTS_l))
OUTPUTS_LINE1_GEN_lt := $(addsuffix .line1.gen.tmstp, $(OUTPUTS_l))
OUTPUTS_ALU_GEN_lt := $(addsuffix .alu.gen.tmstp, $(OUTPUTS_l))
OUTPUTS_SVA_GEN_lt := $(addsuffix .sva.gen.tmstp, $(OUTPUTS_l))
# Simple VCF files.
OUTPUTS_HERVK_VCF := $(HERVK_DISCOVERY_d)/HERVK.final_comp.vcf
OUTPUTS_LINE1_VCF := $(LINE1_DISCOVERY_d)/LINE1.final_comp.vcf
OUTPUTS_ALU_VCF := $(ALU_DISCOVERY_d)/ALU.final_comp.vcf
OUTPUTS_SVA_VCF := $(SVA_DISCOVERY_d)/SVA.final_comp.vcf
# Lazzy evaluation variable.
REQ = $(filter %$(*F)$(SFX), $(INPUTS_l))
# Last preamble command: export all.
export
############################## DEBUG CODE ######################################
ifeq ($(DBG),yes)
$(info ****************************** DEBUG *******************************************)
$(info USER:$(USER).)
$(info DATE:$(DATE).)
$(info )
$(info General App variables.)
$(info APP:$(APP).)
$(info VERSION:$(VERSION).)
$(info ID:$(ID).)
$(info )
$(info Current paths.)
$(info ROOT_DIR:$(ROOT_DIR))
$(info RUNNING_DIR:$(RUNNING_DIR))
$(info CURDIR:$(CURDIR).)
$(info PWD:$(PWD).)
$(info prefix:$(prefix).)
$(info )
$(info PATH:$(PATH).)
$(info )
$(info Configuration files.)
$(info CONFIGFILE:$(CONFIGFILE).)
$(info DFT_CONFIG:$(DFT_CONFIG).)
$(info CONFIG_f:$(CONFIG_f).)
$(info )
$(info Main runtime parameters.)
$(info ENCAPSULATE:$(ENCAPSULATE).)
$(info CLOUDERIZE:$(CLOUDERIZE).)
$(info CLOUDFILE:$(CLOUDFILE).)
$(info DOCKERIZE:$(DOCKERIZE).)
$(info DOCKERFILE:$(DOCKERFILE).)
$(info IMAGE:$(IMAGE).)
$(info MAKERIZE:$(MAKERIZE).)
$(info MAKEFILE:$(MAKEFILE).)
$(info TARBALL:$(TARBALL).)
$(info )
$(info CMD:$(CMD).)
$(info )
$(info INFRASTRUCTURE_dl:$(INFRASTRUCTURE_dl).)
$(info )
$(info Inputs and arguments.)
$(info SFX:$(SFX).)
$(info INPUT:$(INPUT).)
$(info INPUTS_PROCESSED:$(INPUTS_PROCESSED).)
$(info INPUTS_l:$(INPUTS_l).)
$(info OUTPUTS_l:$(OUTPUTS_l).)
$(info )
$(info ARGS:$(ARGS).)
$(info CAPSULE_GET:$(CAPSULE_GET).)
$(info REFERENCE_GENOME:$(REFERENCE_GENOME).)
$(info ********************************************************************************)
endif
# Emergency estop.
ifeq ($(STP),yes)
$(error Emergency stop)
endif
############################## GENERAL TARGETS #################################
help:
@$(ECHO) "Usage:\n"
@$(ECHO) "\tmake [options] target [ARGS=\"arg1 arg2 ...\"]"
$(APP): $(USE_MODE) # app_docker_run or app_native_run
@$(ECHO) "All done."
app_docker_run: image_run
app_native_run: app_has inputs | infra internet_has
@$(ECHO) "Running $(APP) natively ..."
#$(APP) $(ARGS)
@$(ECHO) "Done.\n"
app_has: $(APP_GET) # app_install.
@$(ECHO) "This system has $(APP).\n"
app_install: app_build
@$(ECHO) "Installing $(APP)."
#install $(APP)
@$(ECHO) "Done.\n"
app_build: app_deps tarball_has
@$(ECHO) "Building $(APP)."
#cd $(TARBALL)
#./configure
#$(MAKE)
@$(ECHO) "Done.\n"
tarball_has: $(TARBALL_GET) # tarball or repo
@$(ECHO) "This system has $(APP) tarball.\n"
tarball: $(TARBALL)
$(TARBALL): | internet_has
@$(ECHO) "Downloading tarball for $(APP)-$(VERSION) from $<."
wget $(REPO)/archive/master.tar.gz
#tar xzvf $(notdir $<) # -C $(TMP_d)
@$(ECHO) "Done.\n"
repo: | git_has internet_has
@$(ECHO) "Cloning repository of $(APP)-$(VERSION) from $<."
#git clone $<
@$(ECHO) "Done.\n"
app_deps: #$(APP_DEPS_GET)
@$(ECHO) "This system has the $(APP) dependecies.\n"
internet_has: $(INTERNET_GET) # internet_configure
@$(ECHO) "This system has internet connection.\n"
internet_configure:
@$(ECHO) "Trying to configure system's internet..."
#systemctl ...
@$(ECHO) "ERROR: You need to have internet access to proceed."
exit 1
#infra: | $(CAPSULE) $(INFRASTRUCTURE_dl)
#$(CAPSULE) $(INFRASTRUCTURE_dl):
# @$(ECHO) "Creating directory $@."
# #$(MKDIR) $@
# @$(ECHO) "Done.\n"
clean: | $(INFRASTRUCTURE_dl)
@$(ECHO) "Removing directory $@."
#$(RM) $@
@$(ECHO) "Done.\n"
inputs: #$(INPUTS)
@$(ECHO) "Validating inputs."
#./validate.sh jhgkjh
@$(ECHO) "Done.\n"
test:
@$(ECHO) "This is a simple test for arguments:\"$(ARGS)\"."
# Obligatory targets.
.PHONY:
############################## GIT SPECIFIC TARGETS ############################
git_has:
############################## DOCKER SPECIFIC TARGETS #########################
image_run: docker_has image_has | $(INFRASTRUCTURE_dl) # internet_has
@$(ECHO) "Running docker image $(IMAGE) ..."
#$(DOCKER_RUN) $(DOCKER_ARGS) $(IMAGE) $(ARGS)
@$(ECHO) "Done.\n"
image_has: $(IMAGE_GET) # image_build or image_pull
@$(ECHO) "This system has docker image $(IMAGE).\n"
image_build: docker_has dockerfile_has | internet_has
@$(ECHO) "Building Sandy..."
#$(DOCKER_BUILD) -t $(IMAGE) - < $(DOCKERFILE)
@$(ECHO) "Done.\n"
dockerfile_has: $(DOCKERFILE_GET) # dockerfile_get
@$(ECHO) "This system has dockerfile for image $(IMAGE).\n"
dockerfile_get:
@$(ECHO) "Processing Dockerfile for $(APP).\n"
@$(ECHO) "Done.\n"
image_pull: docker_has | internet_has
@$(ECHO) "Pulling Docker image: $(IMAGE)..."
#docker pull $(IMAGE)
@$(ECHO) "Done.\n"
docker_has: $(DOCKER_GET) # docker_install
@$(ECHO) "This system has docker.\n"
docker_install: docker_build
@$(ECHO) "Installing Docker..."
#cd $(DOCKER_TARBALL)
#./configure
#$(MAKE) && $(MAKE) install
#sudo cp $(subst .tgz,,$(DOCKER_TARBALL))/* /usr/bin/
#sudo dockerd &
@$(ECHO) "Done.\n"
docker_build: $(DOCKER_TARBALL)
$(DOCKER_TARBALL): | internet_has $(TMP_d)
@$(ECHO) "Downloading and unpacking Docker tarball..."
#wget $(DOCKER_TARBALL_URL) -P $@
#tar xzvf $@ -C $(TMP_d)
#$(ECHO) "Done.\n"
cpanm_has: $(CPANM_GET)
@$(ECHO) "This system has cpanm.\n"
cpanm_install: $(CPANM_MAKEFILE) # cpanm.mk
@$(ECHO) "Installing cpanm.\n"
#$(MAKE) -f $(scripts)/cpanm.mk $<
@$(ECHO) "Done.\n"
# Obligatory targets.
.PHONY:
############################## OPERATIONAL TARGETS #############################
all: publish
$(ECHO) "All done."
publish: plot
$(ECHO) "Publishing data..."
# adfvadf
$(ECHO) "Done.\n"
plot: modelate
$(ECHO) "Ploting data..."
modelate: data
$(ECHO) "Modelating data..."
data:# create prepare2 search convert sort3 index3
$(ECHO) "Agregating data..."
index3:
$(ECHO) "Indexing data..."
sort3:
$(ECHO) "Sorting data..."
convert:
$(ECHO) "Converting data..."
search:
$(ECHO) "Searching data..."
prepare2:
$(ECHO) "Preparing data ..."
create: validate
$(ECHO) "Creating data ..."
validate2:
$(ECHO) "Validating data ..."
############################## APP SPECIFIC TARGETS ############################
$(PDF_fl): %.pdf: $(TSV_fl)
$(ECHO) "Training model ..."
R --vanilla --slave --args $< $@ < $(R_MODEL)
$(ECHO) "Done.\n"
$(TSV_fl): %.tsv: %.sorted.bam | index_ref
$(ECHO) "Searching on genome from the FASTA file $< ..."
perl $(scripts)/neopipe.pl search -i $< -d $(REFERENCE_PERLDB) \
-a $(VARIATIONS_FILE) -j $(JOBS) > $@
$(ECHO) "Done.\n"
index_ref: $(REFERENCE_FASTA)
$(ECHO) "Indexing reference genome from the FASTA file $< ..."
perl $(scripts)/neopipe.pl index -i $(REFERENCE_FASTA) -d $(outputs)/$(basename $(REFERENCE_FASTA)).perldb -j $(JOBS)
$(ECHO) "Done.\n"
index2: $(SORTED_BAM_BAI_fl)
$(ECHO) "All BAI files indexed ..."
$(SORTED_BAM_BAI_fl): %.sorted.bam.bai: %.sorted.bam
$(ECHO) "Indexing $< ..."
samtools index -@ 10 $< $@
$(ECHO) "Done.\n"
sort2: $(SORTED_BAM_fl)
$(ECHO) "All BAM files sorted ..."
$(SORTED_BAM_fl): %.sorted.bam: %.sam
$(ECHO) "Sorting $< ..."
samtools sort -O BAM -m 2G -@ 12 $< -o $@
#touch $@
$(ECHO) "Done.\n"
align: $(SAM_fl)
$(ECHO) "All FASTq files aligned ..."
$(BAM_fl): %.bam: %_R1_001.fastq.gz
bwa mem -t 12 $(FASTA) $< $(<:_R1_001.fastq.gz=_R2_001.fastq.gz) > $@
#touch $@
$(ECHO) "Done.\n"
$(SAM_fl): %.sam: %_R1_001.fastq.gz
bwa mem -t 12 $(FASTA) $< $(<:_R1_001.fastq.gz=_R2_001.fastq.gz) > $@
#touch $@
$(ECHO) "Done.\n"
simulate2: $(FASTQ_fl)
$(ECHO) "All files created ..."
.SECONDEXPANSION:
$(FASTQ_fl): %_R1_001.fastq.gz: $$(REQ) $(FASTA) $(IMAGE_ALTERATE) | $(CAPSULE)
$(ECHO) "Preparing data ..."
$(MAKE) -f $(SUB_MAKE) all prefix="$(prefix)" DBG="no" STP="no" \
IMAGE="$(if $(IMAGE_ALTERATE),$(IMAGE_ALT),$(IMAGE))" ARGS="$(ARGS)" -j $(JOBS)
#touch $@
$(ECHO) "Done.\n"
$(PARAMS_l):
image_alterate: image_register
$(ECHO) "Commit the altered image $(IMAGE) as $(IMAGE_ALT)."
docker commit $(CONTAINER_ID) $(IMAGE_ALT)
docker rm $(CONTAINER_ID)
$(ECHO) "Done.\n"
image_register: ARGS := variation add $(VARIATIONS) $(notdir $(VARIATIONS_FILE))
image_register: $(VARIATIONS_FILE)
$(ECHO) "Alterate image $(IMAGE) to register variation file: $<."
docker run -ti -w /home -v $<:/home/$(notdir $<) $(IMAGE) $(ARGS)
$(ECHO) "Done.\n"
docker_run: | infra
$(info )
$(info Run docker image with MELT command.)
$(DOCKER_RUN) \
$(DOCKER_FLAGS) \
-u 1541:1000 \
-w $(C_BASE_d) \
-v $(H_CONFIG_d):$(C_CONFIG_d) \
-v $(H_INPUTS_d):$(C_INPUTS_d) \
-v $(H_OUTPUTS_d):$(C_OUTPUTS_d) \
-v $(H_ASSETS_d):$(C_ASSETS_d) \
-v $(H_REFERENCE_d):$(C_REFERENCE_d) \
-v $(H_ANNOTATION_d):$(C_ANNOTATION_d) \
-v $(H_EXTRA_d):$(C_EXTRA_d) \
-v $(H_TMP_d):$(C_TMP_d) \
$(PIPELINE) $(ARGS)
# Obligatory targets.
.PHONY:
############################## MELT MAIN TARGETS ###############################
vcf: all_vcf
$(info )
$(info $(CALL) All done!)
############################## MAKE VCF ########################################
# Note: VCF are made for all BAMs together, so it can't run in parallel.
# Token target:
all_vcf: hervk_vcf line1_vcf alu_vcf sva_vcf
hervk_vcf: $(OUTPUTS_HERVK_VCF)
line1_vcf: $(OUTPUTS_LINE1_VCF)
alu_vcf: $(OUTPUTS_ALU_VCF)
sva_vcf: $(OUTPUTS_SVA_VCF)
$(OUTPUTS_HERVK_VCF): %HERVK.final_comp.vcf: $(OUTPUTS_HERVK_GEN_lt)
$(info )
$(info $(CALL) Create VCF for HERVK from files $^.)
$(MAKE_VCF) \
-genotypingdir $(HERVK_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(HERVK_ZIP) \
-w $(HERVK_DISCOVERY_d) \
-p $(HERVK_DISCOVERY_d) \
-o $(@D)
$(OUTPUTS_LINE1_VCF): %LINE1.final_comp.vcf: $(OUTPUTS_LINE1_GEN_lt)
$(info )
$(info $(CALL) Create VCF for LINE1 from files $^.)
$(MAKE_VCF) \
-genotypingdir $(LINE1_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(LINE1_ZIP) \
-w $(LINE1_DISCOVERY_d) \
-p $(LINE1_DISCOVERY_d) \
-o $(@D)
$(OUTPUTS_ALU_VCF): %ALU.final_comp.vcf: $(OUTPUTS_ALU_GEN_lt)
$(info )
$(info $(CALL) Create VCF for ALU from files $^.)
$(MAKE_VCF) \
-genotypingdir $(ALU_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(ALU_ZIP) \
-w $(ALU_DISCOVERY_d) \
-p $(ALU_DISCOVERY_d) \
-o $(@D)
$(OUTPUTS_SVA_VCF): %SVA.final_comp.vcf: $(OUTPUTS_SVA_GEN_lt)
$(info )
$(info $(CALL) Create VCF for SVA from files $^.)
$(MAKE_VCF) \
-genotypingdir $(SVA_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(SVA_ZIP) \
-w $(SVA_DISCOVERY_d) \
-p $(SVA_DISCOVERY_d) \
-o $(@D)
############################## GENOTYPING ######################################
# Token target:
all_gen: hervk_gen line1_gen alu_gen sva_gen
hervk_gen: $(OUTPUTS_HERVK_GEN_lt)
line1_gen: $(OUTPUTS_LINE1_GEN_lt)
alu_gen: $(OUTPUTS_ALU_GEN_lt)
sva_gen: $(OUTPUTS_SVA_GEN_lt)
$(OUTPUTS_HERVK_GEN_lt): %.bam.hervk.gen.tmstp: %.bam $(OUTPUTS_HERVK_GRP_t)
$(info )
$(info $(CALL) Genotyping HERVK in file $<.)
$(GENOTYPE) \
-bamfile $< \
-h $(REFERENCE_GENOME) \
-t $(HERVK_ZIP) \
-w $(HERVK_DISCOVERY_d) \
-p $(HERVK_DISCOVERY_d)
touch $@
$(OUTPUTS_LINE1_GEN_lt): %.bam.line1.gen.tmstp: %.bam $(OUTPUTS_LINE1_GRP_t)
$(info )
$(info $(CALL) Genotyping LINE1 in file $<.)
$(GENOTYPE) \
-bamfile $< \
-h $(REFERENCE_GENOME) \
-t $(LINE1_ZIP) \
-w $(LINE1_DISCOVERY_d) \
-p $(LINE1_DISCOVERY_d)
touch $@
$(OUTPUTS_ALU_GEN_lt): %.bam.alu.gen.tmstp: %.bam $(OUTPUTS_ALU_GRP_t)
$(info )
$(info $(CALL) Genotyping ALU in file $<.)
$(GENOTYPE) \
-bamfile $< \
-h $(REFERENCE_GENOME) \
-t $(ALU_ZIP) \
-w $(ALU_DISCOVERY_d) \
-p $(ALU_DISCOVERY_d)
touch $@
$(OUTPUTS_SVA_GEN_lt): %.bam.sva.gen.tmstp: %.bam $(OUTPUTS_SVA_GRP_t)
$(info )
$(info $(CALL) Genotyping SVA in file $<.)
$(GENOTYPE) \
-bamfile $< \
-h $(REFERENCE_GENOME) \
-t $(SVA_ZIP) \
-w $(SVA_DISCOVERY_d) \
-p $(SVA_DISCOVERY_d)
touch $@
############################## GROUP ANALYSES ##################################
# Note: Group analysis are made for all together, so it can't run in parallel.
# Token target:
all_group: hervk_group line1_group alu_group sva_group
hervk_group: $(OUTPUTS_HERVK_GRP_t)
line1_group: $(OUTPUTS_LINE1_GRP_t)
alu_group: $(OUTPUTS_ALU_GRP_t)
sva_group: $(OUTPUTS_SVA_GRP_t)
$(OUTPUTS_HERVK_GRP_t): $(OUTPUTS_HERVK_INDIV_lt) | $(TMSTP_d)
$(info )
$(info $(CALL) Group analysis of HERVK on files $^.)
$(GROUP_ANALYSIS) \
-discoverydir $(HERVK_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(HERVK_ZIP) \
-w $(HERVK_DISCOVERY_d) \
-n $(REFERENCE_BED)
touch $@
$(OUTPUTS_LINE1_GRP_t): $(OUTPUTS_LINE1_INDIV_lt) | $(TMSTP_d)
$(info )
$(info $(CALL) Group analysis of LINE1 on files $^.)
$(GROUP_ANALYSIS) \
-discoverydir $(LINE1_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(LINE1_ZIP) \
-w $(LINE1_DISCOVERY_d) \
-n $(REFERENCE_BED)
touch $@
$(OUTPUTS_ALU_GRP_t): $(OUTPUTS_ALU_INDIV_lt) | $(TMSTP_d)
$(info )
$(info $(CALL) Group analysis of ALU on files $^.)
$(GROUP_ANALYSIS) \
-discoverydir $(ALU_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(ALU_ZIP) \
-w $(ALU_DISCOVERY_d) \
-n $(REFERENCE_BED)
touch $@
$(OUTPUTS_SVA_GRP_t): $(OUTPUTS_SVA_INDIV_lt) | $(TMSTP_d)
$(info )
$(info $(CALL) Group analysis of SVA on files $^.)
$(GROUP_ANALYSIS) \
-discoverydir $(SVA_DISCOVERY_d) \
-h $(REFERENCE_GENOME) \
-t $(SVA_ZIP) \
-w $(SVA_DISCOVERY_d) \
-n $(REFERENCE_BED)
touch $@
############################## INDIVIDUAL ANALYSES #############################
# Token target:
all_indiv: hervk_indiv line1_indiv alu_indiv sva_indiv
hervk_indiv: $(OUTPUTS_HERVK_INDIV_lt)
line1_indiv: $(OUTPUTS_LINE1_INDIV_lt)
alu_indiv: $(OUTPUTS_ALU_INDIV_lt)
sva_indiv: $(OUTPUTS_SVA_INDIV_lt)
# Setting timestamps for several MEI types processes.
$(OUTPUTS_HERVK_INDIV_lt): %.bam.hervk.indiv.tmstp: %.bam %.bam.disc