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See the following links with information about the execution on a cluster:
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See also the example project on Github: https://github.com/Deltares/FAIR-data-example-project |
Instruction
Running Snakemake
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import os ####SETTINGS#### localrules: create_sims, grid, locations # these rules are not submitted wind_speed_list ## TODO this list also in the script create sims. How to access this list in a python script? wind_speed_list = [30, 20] win #= variations True ####End result#### rule all: input: output_bot=os.path.join('data','3-input','vzm-j19_6-v1a_20m.bot'), output_fxw=path_fig=expand("reports/U{wind_speed}.png", wind_speed=wind_speed_list), rule analyse: input: path="data/4-output/U{wind_speed}/U{wind_speed}_p1.tab" output: path_fig="reports/U{wind_speed}.png" script: os.path.join('datasrc','34-inputanalyze','vzm-j19_6-v1a_20m.fxwanalyse.py'), output_p1rule run: input: output_bot=os.path.join('data','3-input','p1bed.xynbot'), output_p2p1=os.path.join('data','3-input','p2p1.xyn'), path_sims=expand("data/4-output/U{wind_speed}/U{wind_speed}.swn", wind_speed=wind_speed_list), output: res=expand("data/4-output/U{wind_speed}/U{wind_speed}_p1.tab", wind_speed=wind_speed_list) rule run: if not output: res=win: shell("data/4-output/U{wildcards.wind_speed}/run_SWAN.sh U{wildcards.wind_speed}_p1.tab" shell: ") else: shell("cd data/4-output/U{wildcards.wind_speed}/swan4131A1c7.sh && copy U{wildcards.wind_speed}.swn INPUT && call ..\\..\\..\\bin\\swan_4131A_1_del_w64_i18_omp.exe ") rule create_sims: input: bot=os.path.join('data','3-input','vzm-j19_6-v1a_20mbed.bot'), p1=os.path.join('data','3-input','p1.xyn'), path_template = os.path.join('config','template') output: path_sims=expand("data/4-output/U{wind_speed}/U{wind_speed}.swn", wind_speed=wind_speed_list) script: os.path.join('src','1-prepare','create_sims.py') rule grid: input: path_bot=os.path.join('data','1-external','vzm-j19_6-v1a_20mbed.bot'), path_fxw=os.path.join('data','1-external','vzm-j19_6-v1a_20mobs.fxw'), output: output_bot=os.path.join('data','3-input','vzm-j19_6-v1a_20mbed.bot'), output_fxw=os.path.join('data','3-input','vzm-j19_6-v1a_20mobs.fxw'), script: os.path.join('src','1-prepare','create_grid.py') rule locations: input: path_p1=os.path.join('data','1-external','p1.xyn'), path_p2=os.path.join('data','1-external','p2.xyn'), output: output_p1=os.path.join('data','3-input','p1.xyn'), output_p2=os.path.join('data','3-input','p2.xyn'), script: os.path.join('src','1-prepare','create_output_locations.py') |
This dummy project required the execution of the following python scripts before the simulations are submitted:.
Create_grid.py
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import os import shutil debugpath_bot = False if debug: pathsnakemake.input.path_bot path_fxw = snakemake.input.path_fxw output_bot = ossnakemake.path.join('..','..','data','1-external','vzm-j19_6-v1a_20m.bot') path_fxw = os.path.join('..','..','data','1-external','vzm-j19_6-v1a_20m.fxw') output_bot = os.path.join('..','..','data','3-input','vzm-j19_6-v1a_20m.bot') output_fxw = os.path.join('..','..','data','3-input','vzm-j19_6-v1a_20m.fxw') else: path_bot = snakemake.input.path_bot path_fxw = snakemake.input.path_fxw output_bot = snakemake.output.output_bot output_fxw = snakemake.output.output_fxw print('copy from:') print(path_bot) print('copy to:') print(output_bot) ## In this demo only files are copied, but in reality bed and fxw are created based on external data. shutil.copyfile(path_bot, output_bot) shutil.copyfile(path_fxw, output_fxw)output.output_bot output_fxw = snakemake.output.output_fxw ## In this demo only files are copied, but in reality bed and fxw are created based on external data. shutil.copyfile(path_bot, output_bot) shutil.copyfile(path_fxw, output_fxw) |
create_output_locations.py
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import os
import shutil
path_p1 = snakemake.input.path_p1
path_p2 = snakemake.input.path_p2
output_p1 = snakemake.output.output_p1
output_p2 = snakemake.output.output_p2
## In this demo only files are copied, but in reality bed and fxw are created based on external data.
shutil.copyfile(path_p1, output_p1)
shutil.copyfile(path_p2, output_p2) |
create_sims.py
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import os
import numpy as np
from shutil import copyfile
from mako.template import Template
def render_template(data,template):
'''
Render template
input:
data: dictionary with variables to render
template: template file
'''
with open(template) as f:
template = f.read()
##
tmpl = Template(text=template)
with open(os.path.join(data['output_path'], '{}.{}'.format(data['fname'],data['extension']) ),mode='w') as f:
f.write(tmpl.render(**data))
path_sims = snakemake.output.path_sims
path_template = snakemake.input.path_template
## if file exists overwrite
overwrite = False
swan_template = 'swan_template_final.swn'
# =============================================================================
# wave conditions
# =============================================================================
wind_speed_list = [30, 20]
# =============================================================================
# create sims
# =============================================================================
## template file
template = os.path.join(path_template,swan_template)
run_condition = {'water_level':[],
'wind_speed':[],
'wind_dir':[]}
## make combinations
for ii, item in enumerate(wind_speed_list):
## get conditions
wind_speed = item
fname = 'U{}'.format(wind_speed)
## data for template
data = {'output_path':os.path.dirname(path_sims[ii]),
'extension':'swn',
'variant':'A',
'fname':fname,
'wind_speed': wind_speed,
'wind_dir': 180,
'water_level': 0}
## skip if file already exists
if os.path.exists(os.path.join(path_sims[ii], '{}.swn'.format(fname))) and overwrite:
print('skipped {}'.format(fname))
continue
## render template
render_template(data,template)
## copy swan_run
copyfile(os.path.join(path_template,'run_SWAN.sh'), os.path.join(os.path.dirname(path_sims[ii]),'run_SWAN.sh'))
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