plasmidid-software
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Table of Contents
plasmidid
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.
Information
- Version: 1.6.3
- Added: September, 2020
Usage
See versions of plasmidid that are available:
$ module avail plasmidid
Load one version into your environment and run it:
$ module load plasmidid/1.6.3 $ plasmidID
Installation
Notes from the sysadmin during installation.
$ cd /tmp $ git clone --recursive https://github.com/BU-ISCIII/plasmidID.git -b v1.6.3 $ sudo mkdir -p /export/apps/plasmidid/1.6.3 $ sudo chown aorth /export/apps/plasmidid/1.6.3 $ python3 -m venv /export/apps/plasmidid/1.6.3 $ source /export/apps/plasmidid/1.6.3/bin/activate # a few python modules as gleaned from the plasmidID Bioconda recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/plasmidid/meta.yaml $ pip install biopython pandas scipy scikit-learn tabulate $ cd plasmidID $ sudo cp -r * /export/apps/plasmidid/1.6.3 $ sudo chown -R root:root /export/apps/plasmidid/1.6.3
After installation I tested the pipeline with the test data:
$ module load plasmidid/1.6.3 $ cp -r /export/apps/plasmidid/1.6.3/TEST_DATA /tmp $ cd /tmp $ plasmidID \ -1 TEST_DATA/KPN_TEST_R1.fastq.gz \ -2 TEST_DATA/KPN_TEST_R2.fastq.gz \ -d TEST_DATA/plasmids_TEST_database.fasta \ -c TEST_DATA/contigs_KPN_TEST.fasta \ --no-trim \ -s KPN \ -T 4
plasmidid-software.1600426885.txt.gz · Last modified: 2020/09/18 11:01 by aorth