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setup.py
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setup.py
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from urllib.request import urlretrieve
from stat import S_IXUSR, S_IXOTH, S_IXGRP, S_IRUSR, S_IROTH, S_IRGRP, S_IWUSR
from os import mkdir, chmod, remove, chdir
from os.path import dirname, abspath, join, exists, basename
from zipfile import ZipFile
import tarfile
from setuptools import setup, find_packages
import subprocess
project_root = dirname(abspath(__file__))
lib_dir = join(project_root, 'rnannot', 'lib')
if not exists(lib_dir):
mkdir(lib_dir)
print('Downloading fastQC ...')
urlretrieve(
'https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip',
join(lib_dir, 'fastqc_v0.11.7.zip'))
print('Downloading Trimmomatic ...')
urlretrieve(
'http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip',
join(lib_dir, 'Trimmomatic-0.38.zip'))
print('Downloading HISAT2 ...')
urlretrieve(
'https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-Linux_x86_64/download',
join(lib_dir, 'hisat2-2.1.0-Linux_x86_64.zip'))
print('Downloading BBMap ...')
urlretrieve(
'https://downloads.sourceforge.net/project/bbmap/BBMap_38.00.tar.gz',
join(lib_dir, 'BBMap_38.00.tar.gz'))
print('Downloading Picard ...')
urlretrieve(
'https://github.com/broadinstitute/picard/releases/download/2.18.7/picard.jar',
join(lib_dir, 'picard.jar'))
print('Downloading GATK v4 ...')
urlretrieve('https://github.com/broadinstitute/gatk/releases/download/4.1.6.0/gatk-4.1.6.0.zip',
join(lib_dir, 'gatk-4.1.6.0.zip'))
print('Downloading bam_to_bigwig ...')
subprocess.run(['git', 'clone', 'https://github.com/NAL-i5K/bam_to_bigwig.git', join(lib_dir, 'bam_to_bigwig')])
print('Downloading regtools ...')
subprocess.run(['git', 'clone', 'https://github.com/griffithlab/regtools', join(lib_dir, 'regtools')])
mkdir(join(lib_dir, 'regtools', 'build'))
chdir(join(lib_dir, 'regtools', 'build'))
subprocess.run(['cmake', '..'])
subprocess.run(['make'])
chdir(join(project_root))
print('Unpacking fastQC ...')
with ZipFile(join(lib_dir, 'fastqc_v0.11.7.zip'), 'r') as zip_ref:
zip_ref.extractall(lib_dir)
# fix the permission of fastqc
chmod(
join(lib_dir, 'FastQC', 'fastqc'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
print('Unpacking Trimmomatic ...')
with ZipFile(join(lib_dir, 'Trimmomatic-0.38.zip'), 'r') as zip_ref:
zip_ref.extractall(lib_dir)
print('Unpacking HISAT2 ...')
with ZipFile(join(lib_dir, 'hisat2-2.1.0-Linux_x86_64.zip'), 'r') as zip_ref:
zip_ref.extractall(lib_dir)
# fix the permission of HISAT2
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2-align-s'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2-align-l'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2-build'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2-build-s'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
chmod(
join(lib_dir, 'hisat2-2.1.0', 'hisat2-build-l'),
S_IXUSR | S_IXOTH | S_IXGRP | S_IRUSR | S_IROTH | S_IRGRP | S_IWUSR)
print('Unpacking BBMap ...')
tar = tarfile.open(join(lib_dir, 'BBMap_38.00.tar.gz'), 'r:gz')
tar.extractall(lib_dir)
tar.close()
print('Unpacking gatk ...')
with ZipFile(join(lib_dir, 'gatk-4.1.6.0.zip'), 'r') as zip_ref:
zip_ref.extractall(lib_dir)
print('Cleaning the files ...')
files = [
'BBMap_38.00.tar.gz', 'fastqc_v0.11.7.zip',
'hisat2-2.1.0-Linux_x86_64.zip', 'Trimmomatic-0.38.zip',
'gatk-4.1.6.0.zip'
]
for f in files:
remove(join(lib_dir, f))
setup(
name='rnannot',
version='0.0.1',
install_requires=['six'],
packages=find_packages('.'),
scripts=['rnannot/RNAseq_annotate.py','rnannot/download_sra_metadata.py'],
include_package_data=True,
author='Yi Hsiao',
author_email='[email protected]',
license='Public Domain',
keywords='RNA-Seq annotation bioinformatics example',
url=
'https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline', # project home page, if any
)