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adding easyconfigs: gff3tool-2.1.0-foss-2022a.eb and patches: GFF3too…
…lkit-2.1.0-remove_hardcode.patch
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Orient
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Oct 24, 2023
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easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| This patch removes the hardcoded part of the setup.py that downloads and installs BLAST+ | ||
| Author: Orient Kružík (INUITS) | ||
| diff -ruN gff3tool-2.1.0_orig/setup.py gff3tool-2.1.0/setup.py | ||
| --- gff3tool-2.1.0_orig/setup.py 2023-10-22 17:15:12.175583000 +0200 | ||
| +++ gff3tool-2.1.0/setup.py 2023-10-22 17:20:48.098956000 +0200 | ||
| @@ -6,69 +6,12 @@ | ||
| """ | ||
| # Always prefer setuptools over distutils | ||
| from setuptools import setup, find_packages | ||
| -from distutils.command.build import build | ||
| # To use a consistent encoding | ||
| from codecs import open | ||
| -from os import path, remove, mkdir | ||
| -import shutil | ||
| -import tarfile | ||
| -try: | ||
| - from urllib.request import urlretrieve | ||
| -except ImportError: | ||
| - from urllib import urlretrieve | ||
| - | ||
| -import platform | ||
| -import sys | ||
| -from wheel.bdist_wheel import bdist_wheel as _bdist_wheel | ||
| - | ||
| +from os import path | ||
|
|
||
| here = path.abspath(path.dirname(__file__)) | ||
|
|
||
| - | ||
| -class bdist_wheel(_bdist_wheel): | ||
| - def finalize_options(self): | ||
| - _bdist_wheel.finalize_options(self) | ||
| - # Mark us as not a pure python package | ||
| - self.root_is_pure = False | ||
| - | ||
| -class CustomBuildCommand(build): | ||
| - def run(self): | ||
| - platform_system = platform.system( | ||
| - ) # Linux: Linux; Mac:Darwin; Windows: Windows | ||
| - | ||
| - blast_path = path.join(here, 'gff3tool', 'lib', 'ncbi-blast+') | ||
| - blast_file = path.join(blast_path, 'blast.tgz') | ||
| - | ||
| - mkdir(blast_path) | ||
| - | ||
| - if platform_system == 'Linux': | ||
| - urlretrieve( | ||
| - 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz', | ||
| - blast_file) | ||
| - elif platform_system == 'Windows': | ||
| - urlretrieve( | ||
| - 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-win64.tar.gz', | ||
| - blast_file) | ||
| - elif platform_system == 'Darwin': | ||
| - urlretrieve( | ||
| - 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz', | ||
| - blast_file) | ||
| - else: | ||
| - sys.error( | ||
| - 'GFF3 Toolkit currently only supports linux, windows, and MacOS' | ||
| - ) | ||
| - | ||
| - tar = tarfile.open(blast_file, 'r:gz') | ||
| - tar.extractall(blast_path) | ||
| - tar.close() | ||
| - | ||
| - extract_path = path.join(blast_path, 'ncbi-blast-2.2.31+') | ||
| - shutil.move(path.join(extract_path, 'bin'), blast_path) | ||
| - if path.exists(blast_file): | ||
| - remove(blast_file) | ||
| - if path.exists(extract_path): | ||
| - shutil.rmtree(extract_path) | ||
| - | ||
| # Get the long description from the README file | ||
| with open(path.join(here, 'README.md'), encoding='utf-8') as f: | ||
| long_description = f.read() | ||
| @@ -170,11 +113,6 @@ | ||
| # | ||
| packages=find_packages(exclude=['contrib', 'docs', 'tests']), # Required | ||
|
|
||
| - cmdclass={ | ||
| - 'build': CustomBuildCommand, | ||
| - 'bdist_wheel': bdist_wheel | ||
| - }, | ||
| - | ||
| # This field lists other packages that your project depends on to run. | ||
| # Any package you put here will be installed by pip when your project is | ||
| # installed, so they must be valid existing projects. |
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easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| easyblock = 'PythonPackage' | ||
|
|
||
| name = 'gff3tool' | ||
| version = '2.1.0' | ||
|
|
||
| homepage = 'https://gff3toolkit.readthedocs.io' | ||
| description = 'Python programs for processing GFF3 files' | ||
|
|
||
| toolchain = {'name': 'foss', 'version': '2022a'} | ||
|
|
||
| sources = ['gff3tool-2.1.0.tar.gz'] | ||
| patches = ['GFF3toolkit-2.1.0-remove_hardcode.patch'] | ||
| checksums = [ | ||
| {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, | ||
| {'GFF3toolkit-2.1.0-remove_hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, | ||
| ] | ||
|
|
||
| local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' | ||
| preinstallopts = 'mkdir -p %s && ' % local_blast_path | ||
| preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path | ||
|
|
||
| dependencies = [ | ||
| ('Python', '3.10.4'), | ||
| ('BLAST+', '2.13.0'), | ||
| ] | ||
|
|
||
| use_pip = True | ||
| sanity_pip_check = True |