====== plasmidid ======
PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

===== Information =====

  * Version: 1.6.5
  * Added: September, 2020
  * Updated: June, 2023
  * Link: https://github.com/BU-ISCIII/plasmidID/wiki

===== Usage =====

See versions that are available:
<code>$ module avail plasmidid</code>

Load one version into your environment and run it:
<code>$ module load plasmidid/1.6.5
$ plasmidID</code>

**Note:** Please use the ''-T'' option to tell plasmidID how many CPU threads it should use or else it will automatically use all the CPUs on the system. This number should match the number of CPUs you requested in your SLURM batch allocation.

===== Installation ======
Notes from the sysadmin during installation.

<code>$ cd /tmp
$ git clone --recursive https://github.com/BU-ISCIII/plasmidID.git -b 1.6.5
$ cd plasmidID
$ sudo mkdir -p /export/apps/plasmidid/1.6.5
$ sudo chown aorth /export/apps/plasmidid/1.6.5
$ module load python/3.9
$ python3 -m venv /export/apps/plasmidid/1.6.5/.venv
$ source /export/apps/plasmidid/1.6.5/.venv/bin/activate
$ pip install --upgrade pip setuptools wheel
$ pip install biopython pandas scipy scikit-learn tabulate
$ sed 's/python$/python3/' bin/*.py
$ cp -r * /export/apps/plasmidid/1.6.5
$ sudo chown -R root:root /export/apps/plasmidid/1.6.5</code>

See the [[https://github.com/bioconda/bioconda-recipes/blob/master/recipes/plasmidid/meta.yaml|bioconda meta.yaml for plasmidid]] for more information.

After installation I tested the pipeline with the included test data:

<code>$ module load plasmidid/1.6.5
$ cp -r /export/apps/plasmidid/1.6.5/test /var/scratch/plasmid-test
$ cd /var/scratch/plasmid-test
$ plasmidID \
     -1 KPN_TEST_R1.fastq.gz  \
     -2 KPN_TEST_R2.fastq.gz \
     -d plasmids_TEST_database.fasta \
     -c contigs_KPN_TEST.fasta \
     --no-trim \
     -s KPN \
     -T 4</code>