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perf: Parallelize download reference #1065

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merged 6 commits into from
Jan 23, 2023
Merged

perf: Parallelize download reference #1065

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e64a9ec
Paralelize download_reference
fevac Jan 20, 2023
1ffe115
Excluded unsupported retries tag due to old snakemake version
fevac Jan 20, 2023
a40070f
Constraint wildcard
fevac Jan 20, 2023
23128ba
Update changelog
fevac Jan 23, 2023
78664b2
Fix output syntax
fevac Jan 23, 2023
029dc6c
Change os by pathlib
fevac Jan 23, 2023
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69 changes: 42 additions & 27 deletions BALSAMIC/workflows/reference.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -194,36 +194,51 @@ download_content = [reference_genome_url, dbsnp_url, hc_vcf_1kg_url,
delly_mappability_findex_url, ascat_gccorrection_url, ascat_chryloci_url, clinvar_url,
somalier_sites_url]

download_dict = dict([(ref.get_output_file, ref) for ref in download_content])

def download_reference_file(output_file):
import requests

ref = download_dict[output_file]
log_file = output_file + ".log"

if ref.url.scheme == "gs":
cmd = "export TMPDIR=/tmp; gsutil cp -L {} {} -".format(log_file,ref.url)
else:
cmd = "wget -a {} -O - {}".format(log_file,ref.url)

if ref.secret:
try:
response = requests.get(ref.url,headers={'Authorization': 'Basic %s' % ref.secret})
download_url = response.json()["url"]
except:
LOG.error("Unable to download {}".format(ref.url))
raise
cmd = "curl -o - '{}'".format(download_url)

if ref.gzip:
cmd += " | gunzip "

cmd += " > {}".format(output_file)
shell(cmd)
ref.write_md5

ref_subdirs = set([ref.output_path for ref in download_content])
ref_files = set([ref.output_file for ref in download_content])

wildcard_constraints:
ref_subdir="|".join(ref_subdirs),
ref_file = "|".join(ref_files),
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rule download_reference:
output:
expand("{output}", output=[ref.get_output_file for ref in download_content])
Path("{ref_subdir}","{ref_file}").as_posix(),
run:
import requests

for ref in download_content:
output_file = ref.get_output_file
log_file = output_file + ".log"

if ref.url.scheme == "gs":
cmd = "export TMPDIR=/tmp; gsutil cp -L {} {} -".format(log_file, ref.url)
else:
cmd = "wget -a {} -O - {}".format(log_file, ref.url)

if ref.secret:
try:
response = requests.get(ref.url, headers={'Authorization': 'Basic %s' % ref.secret })
download_url = response.json()["url"]
except:
LOG.error("Unable to download {}".format(ref.url))
raise
cmd = "curl -o - '{}'".format(download_url)

if ref.gzip:
cmd += " | gunzip "

cmd += " > {}".format(output_file)
shell(cmd)
ref.write_md5
download_reference_file(output[0])




##########################################################
# Preprocess refseq file by fetching relevant columns and
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5 changes: 5 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -5,6 +5,11 @@ Added:
^^^^^^
* Added somalier integration and relatedness check: https://github.com/Clinical-Genomics/BALSAMIC/pull/1017

Changed:
^^^^^^^^
* Parallelize download of reference files https://github.com/Clinical-Genomics/BALSAMIC/pull/1065


Fixed:
^^^^^^
* test_write_json failing locally https://github.com/Clinical-Genomics/BALSAMIC/pull/1063
Expand Down