Differences

This shows you the differences between two versions of the page.

@@ Line 1: / Line 1: @@
+====== 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>

ILRI Research Computing