Comments (7)
It's not built in, but I agree it should be.
If your CNVkit installation is controlled under pip (maybe conda, too), this will show you the version you have installed:
pip list | grep CNVkit
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These will work now -- on the command line:
cnvkit.py version
In Python:
import cnvlib
print cnvlib.__version__
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Hi Eric, thanks for adding this these little tweaks make life a lot easier.
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Thanks.
Q: Acknowledging that I don't fully know the various channels/repositories that Python package can be distributed, how is CNVkit released? When you're saying "will work now", does that mean that CNVkit is pushed out through these channels (e.g. Anaconda etc.) straightaway, or do you mean "will work now [if you install from git source]"?
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@HenrikBengtsson - At the moment it will work if you install from git source. The next release (v0.4.1, soon) will be tagged in git and uploaded to PyPI, the central repository for Python packages, and that will be what you get if you do "pip install -U cnvkit". That will be the first release to include this change.
I actually don't know how/when @chapmanb is updating the conda package at https://binstar.org/bcbio/cnvkit, but if it's not automated then he seems to be doing it very quickly after each PyPI upload.
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On Wed, Apr 29, 2015 at 10:17 AM, Eric Talevich
[email protected] wrote:
@HenrikBengtsson - At the moment it will work if you install from git source. The next release (v0.4.1, soon) will be tagged in git and uploaded to PyPI, the central repository for Python packages, and that will be what you get if you do "pip install -U cnvkit". That will be the first release to include this change.
I actually don't know how/when @chapmanb is updating the conda package at https://binstar.org/bcbio/cnvkit, but if it's not automated then he seems to be doing it very quickly after each PyPI upload.
Thanks for these clarifications; very helpful.
—
Reply to this email directly or view it on GitHub.
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Eric -- thanks for adding these. I manually roll out conda packages after releases so will update whenever you get the new release pushed.
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Related Issues (20)
- baits and target bed file
- How to merge vcfs of different samples?
- Running CNVkit with VCF files
- how to install the cnvkit v0.9.11 by the tar.gz source
- No Results HOT 1
- Installation error HOT 3
- Unable to produce .cnr files HOT 2
- Getting BAF and allelic imbalance in export vcf
- Improper post-processing of segment [bug]
- Unable to use fix without antitarget file for WGS samples
- Merging segments while running pipeline
- `segment` function fails HOT 1
- Somatic CNV calling in case of pre-existing CNVs
- Installation problems HOT 1
- Unable to load BED file with skgenome
- cnvkit.py segment error
- CNVkit segment command RuntimeError: Subprocess command failed
- access command: recommended -s (mingap) value
- Blank plots HOT 1
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