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If you believe there is an issue with the installation of Singularity on Artemis, or an issue with the underlying Artemis hardware, open a High-Performance Computing request via the Service Management Services Portal portal. Tickets requesting support for applications running inside a container will be silently closed.
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spython recipe Dockerfile >> Singularity.trinity |
Next, edit the newly created Singularity image file. Add the Artemis-specific changes to your new singularity image, i.e.
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Bootstrap: docker From: ubuntu:16.04 %files %Dockerfile $SRC/Dockerfile.$TRINITY_VERSION %labels MAINTAINER bhaas@broadinstitute.org %post mkdir /project /scratch |
Next use Singularity to build the image (~30 minutes on my local laptop).
This image/container will be around 2GB as it contains trinity+all the dependencies+the whole operating system. This is fairly standard for Singularity images.
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sudo singularity build Singularity.trinity.build Singularity.trinity |
Now move the build to Artemis
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(with
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scp,
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filezilla,
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etc) and run it with a PBS script:
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#!/bin/bash #PBS -P PROJECT #PBS -l select=1:ncpus=4:mem=4gb #PBS -l walltime=0:10:00 module load singularity/2.6.1 #Change into the directory you executed qsub from cd "$PBS_O_WORKDIR" #Run the singularity image, which contains the program Trinity #The dataset "reads.fq.gz" should be in this directory, #This will create persistent output in a folder called "trinity_out_dir" singularity exec Singularity.trinity.build Trinity --seqType fq --single `pwd`/reads.fq.gz --max_memory 4G --CPU $NCPUS --output `pwd`/trinity_out_dir |
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