metaphlan3tree's People
metaphlan3tree's Issues
Enable removing temporary data when passing a checkpoint
Return species name annotation instead of full label
Evaluate execution of Snakemake pipelines before continuing to next step
When a Snakemake pipeline fails because the individual jobs fail, the pipeline continues despite not having successful. Implement check_point system in Snakefiles to avoid such behaviour.
Add YAML environment file to install all required packages from conda
Current requirements:
- phylophlan
- java8
- pigz
- Python packages: tqdm, snakemake, scikit-bio, ete3
Escape correct replacement of square-bracket species names
Fix installation and path to ASTRAL
ASTRAL currently has no bioconda recipe to be automatically installed. Currently, it involves manually installation and linking into the conda environment.
Add ASTRAL pack to supertree_config of phylophlan
ASTRAL has been currently replaced by RAxML in the 'tree1' section of the phylophlan config because the hard-coded link to an outdated version otherwise crashes the script. Either check whether PhyloPhlAn3 is solving the issue or manually fix it yourself.
Fix after #2
Create Python module installable with pip
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ 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. ๐๐๐
-
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 โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.