rtg-tools: init at 3.12.1 #230394
Merged
rtg-tools: init at 3.12.1 #230394
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Jan 25, 2024
New package for genetics : helps compared variants called by a pipeline to a reference. The only tests not passing are due to a difference in float representation (same value but with different number of digits after decimal). For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. So this package requires NixOS#230394
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Feb 14, 2024
For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. Depends on NixOS#230394
wegank
added
the
2.status: stale
|
This pull request has been mentioned on NixOS Discourse. There might be relevant details there: https://discourse.nixos.org/t/prs-ready-for-review/3032/3701 |
stale
bot
removed
the
2.status: stale
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Mar 29, 2024
For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. Depends on NixOS#230394
|
Thanks a lot for the review. I've formatted the packages using nixfmt-rfc-style, removed the patch (now useless) and use ~/.config/rtg as a configuration directory. The package is now in |
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Mar 30, 2024
For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. Depends on NixOS#230394
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Mar 30, 2024
For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. Depends on NixOS#230394
Comment on lines
43
to
47
| # Use a location outside nix (must be writable) | ||
| sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools' $out/bin/rtg | ||
| sed -i 's|$THIS_DIR/rtg.cfg|$HOME/.config/rtg-tools/rtg.cfg|g' $out/bin/rtg | ||
| # Use nix java | ||
| sed -i 's|RTG_JAVA="java".*|RTG_JAVA="${jdk}/lib/openjdk/bin/java"|' $out/bin/rtg |
There was a problem hiding this comment.
Since we just do simple string replacement here, we should use substituteInPlace with --replace-fail to notice, if the pattern no longer matches.
There was a problem hiding this comment.
I've switched to substituteInPlace, except for appending to a string that I only know how to do it with sed :/
Aleksanaa
reviewed
Apr 1, 2024
A subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Mostly used for vcfeval to compare VCF.
|
Thanks for the feedback. Commits have been squashed, waiting for approval :) |
apraga
added a commit
to apraga/nixpkgs
that referenced
this pull request
Apr 7, 2024
For best results (quality and running time), the authors advice to use RTGtools vcfeval as the engine. Depends on NixOS#230394
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
A subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Mostly used for vcfeval to compare VCF.
Description of changes
Things done
sandbox = trueset innix.conf? (See Nix manual)nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage./result/bin/)