Merge pull request #6 from pvanheus/master Make SalmID package-able (using poetry)
Merge pull request #6 from pvanheus/master
Make SalmID package-able (using poetry)
Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
Python 3
The easy way with homebrew (Linux or MacOS):
brew install brewsci/bio/salmid
Big thanks to Torsten Seemann for including this in homebrew!
Alternatively download from GitHub:
git clone https://github.com/hcdenbakker/SalmID.git
build a wheel using poetry:
cd SalmID poetry build
and install using pip
pip
pip install dist/salmid*.whl
To execute:
SalmID.py -e .fastq.gz
This will perform a SalmID run on all fastq.gz files in the current directory.
SalmID.py -i your_fastq_gz.fastq.gz
This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
SalmID.py -d directory_with_data -e _1.fastq.gz
This will perform a SalmID run on all files in directory ‘directory_with_data’ with extension ‘_1.fastq.gz’
面向沙门氏菌等病原体的基因组分型或鉴定工具，用于公共卫生和微生物检测。
SalmID
Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).
Requirements:
Python 3
Installation:
The easy way with homebrew (Linux or MacOS):
Big thanks to Torsten Seemann for including this in homebrew!
Alternatively download from GitHub:
build a wheel using poetry:
and install using
pipTo execute:
This will perform a SalmID run on all fastq.gz files in the current directory.
This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz)
This will perform a SalmID run on all files in directory ‘directory_with_data’ with extension ‘_1.fastq.gz’
Todo’s and thoughts for future releases: