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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| #!/usr/bin/env python | ||
| #!/usr/bin/env python3 | ||
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| import argparse | ||
| from ruamel.yaml import YAML | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| # EMG-Viral pipeline ENV script | ||
| . /hps/software/users/rdf/metagenomics/service-team/envs/mitrc.sh | ||
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| mitload virify env | ||
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| # virify scripts | ||
| _addpath "/nfs/production/rdf/metagenomics/pipelines/prod/emg-viral-pipeline/bin/" | ||
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| DATABASES="/nfs/production/rdf/metagenomics/pipelines/prod/emg-viral-pipeline/cwl/databases" | ||
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| export VIRSORTER_DATA="${DATABASES}/virsorter-data" | ||
| export ADDITIONAL_HMMS_DATA="${DATABASES}/additional_data_vpHMMs_v2.tsv" | ||
| export HMMSCAN_DATABASE="${DATABASES}/hmmer_databases/vpHMM_database_v3/vpHMM_database_v3.hmm" | ||
| export NCBI_TAX_DB_FILE="${DATABASES}/2020-07-01_ete3_ncbi_tax.sqlite" | ||
| export IMGVR_BLAST_DB="${DATABASES}/IMG_VR_2018-07-01_4" | ||
| export VIRFINDER_MODEL="${DATABASES}/virfinder/VF.modEPV_k8.rda" | ||
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| # workdir | ||
| # required to be shared because | ||
| # - https://toil.readthedocs.io/en/latest/running/hpcEnvironments.html#standard-output-error-from-batch-system-jobs | ||
| # TODO this was seted in virify.sh | ||
| export TMPDIR="/tmp" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,114 @@ | ||
| #!/bin/bash | ||
| #SBATCH --cpus-per-task=1 | ||
| #SBATCH --ntasks=1 | ||
| #SBATCH --mem 8G | ||
| #SBATCH --output="%x_virify.out" | ||
| #SBATCH --error="%x_virify.err" | ||
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| set -e | ||
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| usage() { | ||
| echo "" | ||
| echo "Wrapper script to run the virify workflow using toil-cwl-runner." | ||
| echo "" | ||
| echo "Results will be stored in the output folder," | ||
| echo "under a subfolder named '<job_name>_<timestamp>/'" | ||
| echo "-n Job name [mandatory]." | ||
| echo "-i Input fasta file (full path) [mandatory]." | ||
| echo "-o Output [mandatory]." | ||
| echo "-f Length filter (default 1.0)." | ||
| echo "" | ||
| } | ||
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| # Defaults | ||
| CORES=4 | ||
| MEMORY=8000 # 8GB | ||
| LEN_FILTER=1.0 | ||
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| while getopts "n:i:o:f:h" opt; do | ||
| case $opt in | ||
| n) | ||
| NAME_RUN="$OPTARG" | ||
| if [ -z "$NAME_RUN" ]; then | ||
| echo "" | ||
| echo "ERROR -n cannot be empty." >&2 | ||
| usage | ||
| exit 1 | ||
| fi | ||
| ;; | ||
| i) | ||
| INPUT_FASTA="${OPTARG}" | ||
| if [ -z "${INPUT_FASTA}" ]; then | ||
| echo "" | ||
| echo "ERROR -i cannot be empty." >&2 | ||
| usage | ||
| exit 1 | ||
| fi | ||
| ;; | ||
| o) | ||
| OUTDIR="$OPTARG" | ||
| if [ -z "$OUTDIR" ]; then | ||
| echo "" | ||
| echo "ERROR -o cannot be empty." >&2 | ||
| usage | ||
| exit 1 | ||
| fi | ||
| mkdir -p "$OUTDIR" | ||
| ;; | ||
| f) | ||
| LEN_FILTER="${OPTARG}" | ||
| ;; | ||
| h) | ||
| usage | ||
| exit 0 | ||
| ;; | ||
| :) | ||
| usage | ||
| exit 1 | ||
| ;; | ||
| \?) | ||
| echo "" | ||
| echo "Invalid option -${OPTARG}" >&2 | ||
| usage | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| done | ||
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| if ((OPTIND == 1)); then | ||
| echo "" | ||
| echo "ERROR: No options specified" | ||
| usage | ||
| exit 1 | ||
| fi | ||
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| shift $((OPTIND - 1)) | ||
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| # mandatory params | ||
| if [ -z "${NAME_RUN}" ] || | ||
| [ -z "${INPUT_FASTA}" ] || | ||
| [ -z "${OUTDIR}" ]; then | ||
| echo "" | ||
| echo "ERROR: Missing mandatory parameter." | ||
| usage | ||
| exit 1 | ||
| fi | ||
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| # Embassy env specifics | ||
| WORKDIR="/home/virify/workdir" | ||
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| echo "Submitting the job." | ||
| echo "Workdir: ${WORKDIR}" | ||
| echo "Outdir: ${OUTDIR}/${NAME_RUN}" | ||
| echo "" | ||
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| /home/virify/emg-viral-pipeline/cwl/virify.sh \ | ||
| -e /home/virify/scripts/emg-virify-env.sh \ | ||
| -n "${NAME_RUN}" \ | ||
| -j "${WORKDIR}" \ | ||
| -o "${OUTDIR}" \ | ||
| -f "${LEN_FILTER}" \ | ||
| -c "${CORES}" \ | ||
| -m "${MEMORY}" \ | ||
| -i "${INPUT_FASTA}" \ | ||
| -p embassy |
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