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Code Block
languagebash
titlefargene.sge
#!/bin/sh
#$ -N fargene
#$ -q p28.q
#$ -pe *mpisingle 4
#$ -cwd

module load bioinfo/fargene/0.1

fargene -i reads_1.fastq reads_2.fastq --meta --hmm-model class_b_1_2 -o tutorial_output_1 -p $NSLOTS


Tip
titleNapomena

Napomena

Aplikacija je instalirana i konfigurirana u Python virtualnom okruženju kojeg korisnik može proširiti sa svojim proizvoljnim Python aplikacijama. Nakon učitavanja modula, korisnik dodatne aplikacije instalira s:

Code Block
conda create --prefix $LOCALPKGS python=2.7
conda install --prefix $LOCALPKGS potrebni-python-pkg
ili
pip install --prefix $LOCALPKGS potrebni-python-pkg



Instalacija

Aplikacija je pripremljena u Conda virtualnom okruženju s Python 2.7:

Code Block
titleNaredbe instalacije
source /apps/miniforge3/bin/activate
conda create --prefix /apps/virtenv/fargene python=2.7
conda activate /apps/virtenv/fargene
conda install -c conda-forge -c bioconda fargene