Comments (9)
hey @Zethson is there already a PR for this? How about on bioconda along with already existing Scanpy?
from muon.
We'll have it on confa-forge, I think scanpy is also leaning towards just using conda-forge. There's been one mildly annoying thing that we can't get .tar.gz
source files from PyPI for some versions but I found the way around that should work.
from muon.
@gtca actually, the discussion is open scverse/scanpy#2281
This discussion is also relevant for muon/mudata because nf-core needs updated containers for the nf-core scrnaseq pipeline.
from muon.
Thanks for the reference!
needs updated containers
... which they don't want to build themselves?..
On that note, can't we just use GitHub Container Registry?
from muon.
... which they don't want to build themselves?..
Yes, rightfully so.
On that note, can't we just use GitHub Container Registry?
The question isn't hosting, but keeping the containers up to date. If scverse packages were in bioconda everything would be taken care of magically. But let's add this to the next scverse agenda ok? We have to find a solution here.
from muon.
We can of course build them e.g. on: release
here with actions.
Great, let's discuss in more detail next time then!
from muon.
@gtca I'd be happy if we could solve this at the hackathon. It will be very beneficial for pipelines since they automatically build containers for Bioconda packages etc.
Whether we should go for conda-forge or bioconda is a different matter ^_^
from muon.
Since muon is on conda-forge now, should this issue be closed?
For getting a container built somewhere, something equivalent to scanpy could be done? (BioContainers/multi-package-containers#2209)
from muon.
Huh, since when did that happen?
https://anaconda.org/conda-forge/muon
I had no idea!
from muon.
Related Issues (20)
- "OptionError: 'Pattern matched multiple keys'" traceback in tutorial
- Is being developed? HOT 2
- MOFA error when data has been created using `axis=-1`
- Batch correction for joint modality umap
- Enable `gene_symbols` argument in mu.pl.embedding HOT 1
- Sum duplicate rows in muon.atac.tl.count_fragments_features
- raw is also normalized with clr HOT 4
- How can I concatenate multiple `muon` data samples? HOT 2
- ValueError: could not broadcast input array from shape HOT 2
- float overflow in dsb normalization HOT 1
- dsb normalization results do not replicate results with the original DSBNormalizeProtein function in R
- mu.pl.scatter() fails when providing color
- Add fragment file path to a merged mudata object HOT 1
- ImportError: cannot import name '_compute_connectivities_umap' from 'scanpy.neighbors' HOT 9
- Improve module import time HOT 1
- Test against pre-releases
- Invalid function call in independent component analysis (tl.ica)
- Error with muon import HOT 3
- WNN integration raise error while adding connectivities into mdata.obsp
- Discrete values after using the CLR normalization pt.pp.clr
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from muon.