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Makefile_EXPERIMENTS
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Makefile_EXPERIMENTS
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# =============================================================================================== #
# SRC: Makefile #
# =============================================================================================== #
# =============================================================================================== #
# VARIABLES SECTION #
# =============================================================================================== #
# Here - Specify which python interpreter to employ.
SCRIPT_INTERPETER = python3
# Here - Specify which is the root directory where all results
# from different analyses will be stored, for later investingations
# about results, logs and image files.
BASE_DIR_RESULTS = bioinfo_project
# Here - There are some variable exploited in order
# to run some local tests.
#
# See tasks related to test for more details.
SCRIPT_2_TEST = test_feature.py
TESTS_DIR = tests
# Here - There are two variable used to run the
# classifier tool for genes fusions recognizing:
# - SCRIPT_ANALYSIS, standas for the `main.py` file which is used to
# write the program;
# - PROGRAM_ANALYSIS, is a symbolic link that can be used to run
# the program written above without taking care about how it was implemented
# as weel as without knowing which kind of programming language has been adopted.
#
# See task named `run_analysis` for details how both them have been employed.
SCRIPT_ANALYSIS = main.py
PROGRAM_ANALYSIS = genes_fusions_classifier
# =============================================================================================== #
# VARIABLES DEFINED TO RUN TESTS WITHIN PROPER TASKS #
# =============================================================================================== #
# ---------------------------- ---------------------#
# DATA EXPERIMENT - SECTION #
# ------------------------------------------------- #
ARGS_EXPERIMENT = \
--experimental_mode \
--network_parameters ./models/experimental_simple_models/parameters_dna_seq.json \
--load_network ExperimentalModels \
--sequence_type dna
ARGS_EXPERIMENT_COLAB = \
--experimental_mode \
--network_parameters ./models/experimental_simple_models/parameters_dna_seq.json \
--load_network ExperimentalModels \
--sequence_type dna \
--path_source_data "/content/drive/My Drive/bioinformatics/data-bioinformatics/bins_translated"
# =============================================================================================== #
# TASKS SECTION #
# =============================================================================================== #
# ---------------------------- ---------------------#
# RUN EXPERIMENT - SECTION #
# ------------------------------------------------- #
run_experiment: setup_before_run_task
ln -sfn $(SCRIPT_ANALYSIS) $(PROGRAM_ANALYSIS)
$(SCRIPT_INTERPETER) $(PROGRAM_ANALYSIS) $(ARGS_EXPERIMENT)
run_experiment_on_colab: setup_before_run_task
ln -sfn $(SCRIPT_ANALYSIS) $(PROGRAM_ANALYSIS)
$(SCRIPT_INTERPETER) $(PROGRAM_ANALYSIS) $(ARGS_EXPERIMENT_COLAB)
# ---------------------------- ---------------------#
# MANAGEMENT - SECTION #
# ------------------------------------------------- #
setup_before_run_task:
clear