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changes.mady.by.user Martin Belavić

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VerzijaModul
2.3.8bioinfo/OrthoFinder/2.3.8

Primjer korištenja

2.3.12

bioinfo/OrthoFinder/2.3.12

2.5.4

bioinfo/OrthoFinder/2.5.4

Primjer korištenja

Aplikacija OrthoFinder ne radi na pristupnom čvoru zbog dozvola memorije "/dev/shm" ali uredno radi na radnim čvorovima. Prilikom pokretanja poslova potrebno je staviti opciju "-t $NSLOTS" da se ne raširi po čitavom čvorukako bi se aplikacija širila prema zatraženom broju CPU jezgara/slotova.

Code Block
languagebash
#!/bin/bash
#$ -N test
#$ -pe mpisingle 8
#$ -cwd

module load bioinfo/OrthoFinder/2.35.84

orthofinder -h


Testni primjer aplikacije.

Code Block
languagebash
titleOrthoFinder.sge
#!/bin/bash
#$ -N test
#$ -pe mpisingle 8
#$ -cwd

module load bioinfo/OrthoFinder/2.3.8
orthofinder -t $NSLOTS -f /apps/bioinfo/OrthoFinder/2.3.8/ExampleData/ -o $PWD/test -S diamond

...

Code Block
qsub OrthoFinder.sge


Warning
titleVažno

Nužno je koristiti paralelne okoline *mpisingle jer je aplikacija paralelizirana dijeljenjem memorije (shared memory parallel model)

Parametri instalacije aplikacije

Aplikacija je preuzeta i odpakiranaotpakirana:

Code Block
wget https://github.com/davidemms/OrthoFinder/releases/download/2.3.8/OrthoFinder_glibc-2.15.tar.gz
tar -xvf rthoFinderOrthoFinder_glibc-2.15.tar.gz

Verzija 2.5.4:

Code Block
source /apps/miniforge3/bin/activate
mamba create -p /apps/virtenv/orthofinder/2.5.4 python=3.8 orthofinder=2.5.4 -c bioconda