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

Jump to bottom

Quast: init at 5.0.2 #70401

Merged
merged 1 commit into from Apr 24, 2020
Merged

Quast: init at 5.0.2 #70401

merged 1 commit into from Apr 24, 2020

Conversation

bzizou
Copy link
Contributor

@bzizou bzizou commented Oct 4, 2019

Motivation for this change

This tools is used into my laboratory

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.
Notify maintainers

cc @

risicle
risicle reviewed Oct 6, 2019
View reviewed changes
pkgs/applications/science/biology/quast/default.nix

dontPatchELF = true;

doCheck = false;
Copy link
Contributor

Choose a reason for hiding this comment

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

Please leave a comment of explanation.

@risicle
Copy link
Contributor

risicle commented Oct 6, 2019

Builds on macos 10.13 & executable appears to work, but no tests so I've no confidence it actually works.

Are you sure you wouldn't prefer to expose the executables as quast rather than quast.py?

@bzizou
Copy link
Contributor Author

bzizou commented Oct 7, 2019

The build of this python application is a bit out of standards and it's been a bit hard to package. Tests are disabled because they need a set of data to be downloaded first, so we must run it by hand. Running tests by hand works, despite some "non-fatal" errors
I'm going to check if we can easyly change from quast.py to quast...

@Lassulus
Copy link
Member

Lassulus commented Dec 8, 2019

ping?

@bzizou
Copy link
Contributor Author

bzizou commented Apr 24, 2020

Sorry for the delay... I just added a link quast to the main executable quast.py. I did not rename it, because there's too many references to <script>.py into the Quast documentation and scripts.

Lassulus
Lassulus approved these changes Apr 24, 2020
View reviewed changes
Copy link
Member

@Lassulus Lassulus left a comment

Choose a reason for hiding this comment

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

tested with nix-review, lgtm

@Lassulus Lassulus merged commit d0b1de5 into NixOS:master Apr 24, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@risicle risicle risicle left review comments

@Lassulus Lassulus Lassulus approved these changes

Assignees
No one assigned
Labels
8.has: package (new) 10.rebuild-darwin: 1-10 10.rebuild-darwin: 1 10.rebuild-linux: 1-10 10.rebuild-linux: 1 11.by: package-maintainer
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
3 participants
@bzizou @risicle @Lassulus