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plasmidid-software [2020/09/18 11:40] – aorthplasmidid-software [2023/06/26 14:45] (current) – aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: 1.6.3+  * Version: 1.6.5
   * Added: September, 2020   * Added: September, 2020
 +  * Updated: June, 2023
   * Link: https://github.com/BU-ISCIII/plasmidID/wiki   * Link: https://github.com/BU-ISCIII/plasmidID/wiki
  
 ===== Usage ===== ===== Usage =====
  
-See versions of plasmidid that are available:+See versions that are available:
 <code>$ module avail plasmidid</code> <code>$ module avail plasmidid</code>
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load plasmidid/1.6.3+<code>$ module load plasmidid/1.6.5
 $ plasmidID</code> $ plasmidID</code>
  
-**Note:** Please use the ''--threads'' 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. +**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 ====== ===== Installation ======
 Notes from the sysadmin during installation. Notes from the sysadmin during installation.
  
-<code> +<code>$ cd /tmp 
-$ cd /tmp +$ git clone --recursive https://github.com/BU-ISCIII/plasmidID.git -b 1.6.5
-$ 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 $ cd plasmidID
-$ sudo cp -r * /export/apps/plasmidid/1.6.3 +$ sudo mkdir -p /export/apps/plasmidid/1.6.5 
-$ sudo chown -R root:root /export/apps/plasmidid/1.6.3 +$ sudo chown aorth /export/apps/plasmidid/1.6.5 
-</code>+$ 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 test data:+After installation I tested the pipeline with the included test data:
  
-<code> +<code>$ module load plasmidid/1.6.5 
-$ module load plasmidid/1.6.3 +$ cp -r /export/apps/plasmidid/1.6.5/test /var/scratch/plasmid-test 
-$ cp -r /export/apps/plasmidid/1.6.3/TEST_DATA /tmp +$ cd /var/scratch/plasmid-test
-$ cd /tmp+
 $ plasmidID \ $ plasmidID \
-     -1 TEST_DATA/KPN_TEST_R1.fastq.gz  \ +     -1 KPN_TEST_R1.fastq.gz  \ 
-     -2 TEST_DATA/KPN_TEST_R2.fastq.gz \ +     -2 KPN_TEST_R2.fastq.gz \ 
-     -d TEST_DATA/plasmids_TEST_database.fasta \ +     -d plasmids_TEST_database.fasta \ 
-     -c TEST_DATA/contigs_KPN_TEST.fasta \+     -c contigs_KPN_TEST.fasta \
      --no-trim \      --no-trim \
      -s KPN \      -s KPN \
-     -T 4 +     -T 4</code>
-</code>+
plasmidid-software.1600429206.txt.gz · Last modified: 2020/09/18 11:40 by aorth