TODO: This has been pulling twice the number of cpu that are requested. Need to set srun to twice as many threads as the docker run command. Alan said this could be a java garbage collection problem.
When logged in to login.bioinf.unc.edu pasting the following code in the terminal will run fastqc and then multiqc on all of the contents in a directory:
INPUT_DIR="/your/input/folder"
OUTPUT_DIR="/your/output/folder"
BASE_FILE_NAME="base_name"
TITLE="Title of report"
FASTQ_ENDING="*.fastq.gz"
THREAD_NUM=8
mkdir -p ${OUTPUT_DIR}
srun --pty -c ${THREAD_NUM} --mem-per-cpu 1g -p docker \
docker run --rm=true \
-v /datastore:/datastore:shared \
-e INPUT_DIR="${INPUT_DIR}" \
-e OUTPUT_DIR="${OUTPUT_DIR}" \
-e BASE_FILE_NAME="${BASE_FILE_NAME}" \
-e TITLE="${TITLE}" \
-e FASTQ_ENDING="${FASTQ_ENDING}" \
-e THREAD_NUM="${THREAD_NUM}" \
dockerreg.bioinf.unc.edu:5000/fastmultiqc:3
OR...
srun --pty -c 8 --mem-per-cpu 1g -p docker \
docker run --rm=true \
-v /datastore:/datastore:shared \
-e INPUT_DIR=/datastore/nextgenout4/HTSF/IMGF/170510_UNC21_0420_000000000-B5RJV \
-e OUTPUT_DIR=/datastore/alldata/shiny-server/rstudio-common/dbortone/docker/fastmultiqc/test \
-e BASE_FILE_NAME=base_name \
-e TITLE="Title of report" \
-e FASTQ_ENDING="*.fastq.gz" \
-e THREAD_NUM=8 \
dockerreg.bioinf.unc.edu:5000/fastmultiqc:3
The default values are:
INPUT_DIR="."
OUTPUT_DIR="."
BASE_FILE_NAME="fastmultiqc"
TITLE="FastMultiQC"
FASTQ_ENDING=".fastq.gz"
THREAD_NUM=1
So you can just get away with:
srun --pty -c 1 --mem-per-cpu 1g -p docker \
docker run --rm=true \
-v /datastore:/datastore:shared \
-e INPUT_DIR=/datastore/nextgenout4/HTSF/IMGF/170510_UNC21_0420_000000000-B5RJV \
-e OUTPUT_DIR=/datastore/alldata/shiny-server/rstudio-common/dbortone/docker/fastmultiqc/test \
dockerreg.bioinf.unc.edu:5000/fastmultiqc:2
Content type
Image
Digest
Size
367.9 MB
Last updated
over 6 years ago
docker pull benjaminvincentlab/fastmultiqc:1.3