Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

{bio}[foss-2020b] pdbfixer-1.7 required for alphahelix created #13464

Closed
wants to merge 5 commits into from
Closed

{bio}[foss-2020b] pdbfixer-1.7 required for alphahelix created #13464

Changes from 4 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
504cccc
pdbfixer-1.7 required for alphahelix created
Jul 20, 2021
740566e
Blank line at end of file removed (style)
Jul 20, 2021
8fbbb66
Tidy up of checking, missing h5py dependency added
Jul 28, 2021
6b8caec
Name changed as suggestd to PDBfixer
Jul 30, 2021
2ab3816
Changed name to namelower for sanity checking
Aug 6, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 34 additions & 0 deletions easybuild/easyconfigs/p/PDBfixer/PDBfixer-1.7-foss-2020b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
easyblock = 'PythonPackage'

name = 'PDBfixer'
version = '1.7'

homepage = 'https://github.com/openmm/pdbfixer'
description = """PDBFixer is an easy to use application for fixing problems
in Protein Data Bank files in preparation for simulating them."""

toolchain = {'name': 'foss', 'version': '2020b'}

source_urls = ['https://github.com/openmm/pdbfixer/archive/']
sources = ['v%(version)s.tar.gz']
checksums = ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'] # v1.7.tar.gz

dependencies = [
('Python', '3.8.6'),
('OpenMM', '7.5.1'),
('h5py', '3.1.0'),
]

use_pip = True
download_dep_fail = True

sanity_check_paths = {
'files': ['bin/%(name)s'],
'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/'],
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
'files': ['bin/%(name)s'],
'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/'],
'files': ['bin/%(namelower)s'],
'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/'],

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Done. Thanks for pointing that out.

}

sanity_check_commands = ['%(namelower)s --help']

sanity_pip_check = True

moduleclass = 'bio'