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snp-pipeline-software [2018/06/01 20:58] (current)
aorth created
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 +====== SNP Pipeline ======
  
 +The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
 +
 +===== Information =====
 +
 +  * Version: 1.0.1
 +  * Added: June, 2018
 +  * Link: https://​snp-pipeline.readthedocs.io/​en/​latest/​installation.html
 +
 +===== Usage =====
 +
 +See which versions of snp-pipeline are available:
 +<​code>​$ module avail snp-pipeline</​code>​
 +
 +Load snp-pipeline into your environment:​
 +<​code>​$ module load snp-pipeline/​1.0.1</​code>​
 +
 +===== Installation ======
 +
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ cd /tmp
 +$ module load python/​3.5.3
 +$ sudo mkdir -p /​export/​apps/​snp-pipeline/​1.0.1
 +$ sudo chown -R aorth:aorth /​export/​apps/​snp-pipeline/​1.0.1
 +$ python -m venv /​export/​apps/​snp-pipeline/​1.0.1
 +$ . /​export/​apps/​snp-pipeline/​1.0.1/​bin/​activate
 +$ pip3 install --upgrade pip setuptools
 +$ pip3 install snp-pipeline
 +$ sudo chown -R root:root /​export/​apps/​snp-pipeline/​1.0.1</​code>​
snp-pipeline-software.txt · Last modified: 2018/06/01 20:58 by aorth