Comments (2)
MikkelSchubert
commented on June 27, 2024
Hi Ben,
Sorry for the trouble and thank you for the report!
It seems that I made a mistake while writing the documentation.
Instead of genotyping it should be genotype, as in
paleomix phylo_pipeline genotype+msa+phylogeny makefile.yaml
However, I have to caution that the phylo pipeline is deprecated and slated for removal in the next major release of paleomix (2.0) sometime in the future, due to lack of use and hence development. However, I'll gladly answer your questions and help with any issues you run into.
Best,
Mikkel
from paleomix.
MikkelSchubert
commented on June 27, 2024
I've released a version of paleomix that fixes this (v1.3.8).
Once again thank you for reporting this and do let me know if you run into any other issues.
Best,
Mikkel
from paleomix.
Related Issues (20)
- Alignment to sequence variation graph? HOT 1
- Error running mapDamage in example bam_pipeline HOT 2
- [info] conda instructions for paleomix HOT 1
- Java issue with an updated openjdk version HOT 1
- 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
- BWA backtrack additional options added to samse, not aln HOT 3
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.