plasmidid-software
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plasmidid-software [2020/09/18 11:01] – created aorth | plasmidid-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:// | * Link: https:// | ||
===== Usage ===== | ===== Usage ===== | ||
- | See versions | + | See versions that are available: |
< | < | ||
Load one version into your environment and run it: | Load one version into your environment and run it: | ||
- | < | + | < |
$ plasmidID</ | $ plasmidID</ | ||
+ | |||
+ | **Note:** Please use the '' | ||
===== Installation ====== | ===== Installation ====== | ||
Notes from the sysadmin during installation. | Notes from the sysadmin during installation. | ||
- | < | + | < |
- | $ cd /tmp | + | $ git clone --recursive https:// |
- | $ git clone --recursive https:// | + | |
- | $ sudo mkdir -p / | + | |
- | $ sudo chown aorth / | + | |
- | $ python3 -m venv / | + | |
- | $ source / | + | |
- | # a few python modules as gleaned from the plasmidID Bioconda recipe: https:// | + | |
- | $ pip install biopython pandas scipy scikit-learn tabulate | + | |
$ cd plasmidID | $ cd plasmidID | ||
- | $ sudo cp -r * / | + | $ sudo mkdir -p / |
- | $ sudo chown -R root:root / | + | $ sudo chown aorth / |
- | </ | + | $ module load python/ |
+ | $ python3 -m venv / | ||
+ | $ source / | ||
+ | $ pip install --upgrade pip setuptools wheel | ||
+ | $ pip install biopython pandas scipy scikit-learn tabulate | ||
+ | $ sed ' | ||
+ | $ cp -r * / | ||
+ | $ sudo chown -R root:root / | ||
+ | |||
+ | See the [[https:// | ||
- | After installation I tested the pipeline with the test data: | + | After installation I tested the pipeline with the included |
- | < | + | < |
- | $ module load plasmidid/ | + | $ cp -r / |
- | $ cp -r / | + | $ cd /var/ |
- | $ cd /tmp | + | |
$ plasmidID \ | $ plasmidID \ | ||
- | | + | -1 KPN_TEST_R1.fastq.gz |
- | | + | -2 KPN_TEST_R2.fastq.gz \ |
- | | + | -d plasmids_TEST_database.fasta \ |
- | | + | -c contigs_KPN_TEST.fasta \ |
| | ||
-s KPN \ | -s KPN \ | ||
- | -T 4 | + | -T 4</ |
- | </ | + |
plasmidid-software.1600426885.txt.gz · Last modified: 2020/09/18 11:01 by aorth