Comments (6)
It's definitely not supposed to take that long.
I'll look into it before the end of the week and get back to you.
Best,
Mikkel
from paleomix.
Thanks!
I was able to get it to run once I specified versions for all the channels/dependencies, but that resulted in ~100 conflicts across packages. Currently trying different combinations to see if I can resolve this issue
from paleomix.
Have you tried using mamba instead of vanilla conda?
If not, then I'd highly recommend it. Mamba only takes a few seconds resolve the environment on my system.
I think the problem is that I've consistently been using mamba for a long time, so I didn't notice how bad it had gotten with regular conda. I'll try to see if I cannot improve the situation without having to specify exact versions for everything, but that might end up being the solution.
from paleomix.
I've attached an alternative conda environment to this message, which should solve the problem by pinning the major and minor versions, but not the point release (${major}.${minor}.${point}). It still takes about 4-5 minutes to resolve with conda on my machine, compared to about 2-3 seconds with mamba, which is not optimal, but it's usable. I could reduce it further by pinning the point releases, but that would result in people missing out on bug-fixes in dependencies in between the (very irregular) paleomix releases.
If mamba isn't an option, or if you have time to test it anyway, then please let me know if it works for you.
from paleomix.
I was able to get things up and running with mamba!
from paleomix.
from paleomix.
Related Issues (20)
- thank you, but this message appears with PALEOMIX v.1.2.14 too HOT 3
- readthedocs Documentation incorrectly renders double dash with a 'long' single dash
- "Could not retrieve index file" HOT 1
- paleomix bam_pipeline: error: unrecognized arguments: --gatk_max_threads=1 --progress_ui=running --jre_options= HOT 5
- ImportError: libhts.so.2: cannot open shared object file: No such file or directory HOT 14
- checkpointing HOT 2
- About the MinQuality setting HOT 6
- BOWTIE2 errors in the pipeline HOT 8
- A problem of PALEOMIX 2.0.0-alpha documentation HOT 2
- Should the .rmdup.collapsed.bam and .rmdup.normal.bam be merged? HOT 1
- biobambam2 instead of picard-tools? HOT 10
- Paleomix can not find picard even though it is there HOT 8
- Issue When Employing `RegionsOfInterest`. HOT 6
- similar bams with rescale and non rescale HOT 2
- Phylo pipeline "unknown command" HOT 2
- BWA backtrack additional options added to samse, not aln HOT 3
- Errors running node HOT 2
- Error with trimming SE adapters from sample HOT 2
- Receieved a NodeError while running the pipeline HOT 1
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 paleomix.