Package the tool. Support gatk4 from conda. Add --genome option.#12
Open
vladsavelyev wants to merge 5 commits into
Open
Package the tool. Support gatk4 from conda. Add --genome option.#12vladsavelyev wants to merge 5 commits into
vladsavelyev wants to merge 5 commits into
Conversation
1. The tools can be installed with `./setup.py install`/`./setup.py develop`, or uploaded into PyPI repository to be installed with pip. Corresponding code changes: - rename "modules" to "conpair" to avoid clashes with other libs on system - import module files instead of sourcing with imp - add setup.py - move common functions to conpair/__init__.py - .gitignore eggs/dist/build 2. If `gatk` executable is available in PATH, the tool will assume it's GATK4 and use it directly (unless --gatk or $GATK_JAR set). It allows to use GATK4 from bioconda. 3. GRCh37 is assumed by default, however if you want to run against GRCh38 or mouse genome, you can specify genome build name with `-g`/`--genome` option (as an alternative to referencing the markers file directly with `--markers`)
…mples out into the root folder. Add pip and conda install docs. CONPAIR_DIR env var is not needed
(it prints lines without the 5th column in the pileup output)
stevekm
added a commit
to stevekm/Conpair
that referenced
this pull request
Apr 18, 2025
|
@vladsavelyev, I just wanted to say thank you for doing this work and putting in the PR. It got me out of a bind with some errors I was seeing, hopefully it gets pulled into main eventually. |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Proposing changes that would allow distribution with bioconda and bcbio-nextgen.
./setup.py install/./setup.py develop, or uploaded into PyPI repository to be installed with pip. Corresponding code changes:setup.py,conpair/__init__.py,If
gatkexecutable is available inPATH, the tool will assume it's GATK4 and use it directly (unless--gatkor $GATK_JAR are set). It allows to use GATK4 from bioconda. (resolves Support GATK 4 #11).GRCh37 is assumed by default and corresponding markers files are searched, however if the users want to run against GRCh38 or the mouse genome, they can specify genome build name with
-g/--genomeoption (as an alternative to referencing the markers file directly with--markers).