juanesarango

Having a bedfile like:

initial.bed

chr8	41510743	41513272	uc003xoi.3_exon_0_0_chr8_41510744_r	0	-
chr8	41518947	41519082	uc003xoi.3_exon_1_0_chr8_41518948_r	0	-
chr8	41519393	41519459	uc003xoi.3_exon_2_0_chr8_41519394_r	0	-
chr8	41521176	41521260	uc003xoi.3_exon_3_0_chr8_41521177_r	0	-

juanesarango

#! /bin/bash

BWA_MEM_IMAGE=/juno/work/isabl/local/docker-pcapcore/v0.1.2/docker-pcapcore-v0.1.2.simg
# BWA_MEM_IMAGE=/work/isabl/home/levinem1/software/containers/pcap-core_5.5.0.sif
OUTDIR=`pwd`/$SAMPLE

mkdir -p $OUTDIR/input_data
ln -sf $INPUTDIR/input_data/*.fastq.gz $OUTDIR/input_data

set -euxo pipefail

juanesarango

#! /bin/bash

KEYS_FILE=gpg_keys.txt
MD5_FILE=md5.txt
INDIR=`pwd`
OUTDIR=`pwd`/outdir

mkdir -p $OUTDIR

# Decrypt and decompress

juanesarango

filters = {
    'projects': 324, 
    'submission': 1057,
}

UNIVERSAL_NORMALS = {
    "TD": {
        "HEMEPACT-V3": "I-H-103892-N1-1-D1-3",
        "HEMEPACT-V4": "I-H-100521-N1-1-D1-4",

juanesarango

🐐 Running a local-hosted LLM model in HPC with ollama

💻 Setup

Create a job script that runs an ollama server using singularity:

run_server.sh

#!/bin/bash
#SBATCH -J ollama