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Parasail/en: Difference between revisions
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{{Note | {{Note | ||
| | |From StdEnv/2023 onwards, the parasail-python extension is bundled in the parasail module. However, with StdEnv/2020, the parasail module needs to be loaded for the Python extension to be installed in a virtual environment. | ||
}} | }} | ||
= Usage = | = Usage = | ||
Find the required versions using | |||
{{Command|module spider parasail}} | {{Command|module spider parasail}} | ||
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Run a quick local alignment score comparison between BioPython and parasail. | Run a quick local alignment score comparison between BioPython and parasail. | ||
1. Write the | 1. Write the Python script: | ||
{{File | {{File | ||
|name=parasail-sw.py | |name=parasail-sw.py | ||
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}} | }} | ||
2. | 2. Write the job submission script: | ||
<tabs> | <tabs> | ||
<tab name="Default StdEnv"> | <tab name="Default StdEnv"> | ||
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}} | }} | ||
Install the desired version in your virtual environment: | |||
{{File | {{File | ||
|name=submit-parasail.sh | |name=submit-parasail.sh | ||
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module load StdEnv/2020 gcc parasail/2.5 python/3.10 | module load StdEnv/2020 gcc parasail/2.5 python/3.10 | ||
# Install any other requirements, such as Biopython | # Install any other requirements, such as Biopython: | ||
virtualenv --no-download $SLURM_TMPDIR/env | virtualenv --no-download $SLURM_TMPDIR/env | ||
source $SLURM_TMPDIR/env/bin/activate | source $SLURM_TMPDIR/env/bin/activate | ||
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</tabs> | </tabs> | ||
3. | 3. Submit the job with | ||
{{Command | {{Command | ||
|sbatch submit-parasail.sh | |sbatch submit-parasail.sh | ||
}} | }} | ||
4. | 4. When the job has run, the output will be in the Slurm output file: | ||
{{Command | {{Command | ||
|less slurm-*.out | |less slurm-*.out | ||
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==== Available Python packages ==== | ==== Available Python packages ==== | ||
Other Python packages that depend on parasail will have their requirement satisfied | Other Python packages that depend on parasail will have their requirement satisfied by loading the parasail module: | ||
{{Command | {{Command | ||
|pip list {{!}} grep parasail | |pip list {{!}} grep parasail | ||