Commit 5ab6660e authored by Kevin Kunzmann's avatar Kevin Kunzmann

Merge branch 'zenodo' into 'master'

Zenodo

See merge request !2
parents 855ef4fe 7ff091be
......@@ -3,6 +3,7 @@ output
.snakemake
.Rproj.user
.cache
container.sif
*.zip
*.pdf
*.Rproj
......
singularity: "docker://kkmann/gose-6mo-imputation@sha256:85724229d8f4243aaebd6228e5cc7833474577ac107f9719b00016765f9ee342"
singularity: "container.sif"
configfile: "config.yml"
......
......@@ -2,7 +2,7 @@
"__default__" :
{
"account" : "MRC-BSU-SL2-CPU",
"time" : "06:00:00",
"time" : "03:00:00",
"n" : 1,
"partition" : "bsu-cpu"
}
......
#!/bin/bash
USERNAME="kkmann"
IMAGE="gose-6mo-imputation"
BUILDNAME=$USERNAME/$IMAGE
docker build --no-cache -t $BUILDNAME .
FROM rocker/verse:latest
MAINTAINER Kevin Kunzmann kevin.kunzmann@mrc-bsu.cam.ac.uk
# update apt
RUN sudo apt-get update
# install prerequisits
RUN sudo apt-get -y install libcurl4-openssl-dev curl bzip2
# install required R packages
RUN R -e "install.packages('diagram')"
RUN R -e "install.packages('rstan')"
RUN R -e "install.packages('brms')"
RUN R -e "install.packages('mice')"
RUN R -e "install.packages('ggalluvial')"
RUN R -e "install.packages('caret')"
RUN R -e "install.packages('e1071')"
RUN R -e "install.packages('msm')"
RUN R -e "install.packages('cowplot')"
RUN R -e "install.packages('pander')"
RUN R -e "devtools::install_github('kkmann/describr')"
......@@ -9,3 +9,11 @@ rule download_data:
"""
bash scripts/download_{wildcards.version}.sh
"""
rule download_data_v1_1:
input:
"data/v1.1/df_baseline.rds",
"data/v1.1/df_ctmri.rds",
"data/v1.1/df_imaging.rds",
"data/v1.1/df_labs.rds",
"data/v1.1/df_gose.rds"
#!/bin/bash
set -e
wget https://zenodo.org/record/2600385/files/container.sif
checksum=($(md5sum container.sif))
if [ $checksum != 7db125c9c83621d78981e558546b1e88 ]; then
echo md5 mismatch!
exit 1
fi
Bootstrap: docker
From: rocker/verse:latest
%labels
Maintainer Kevin Kunzmann kevin.kunzmann@mrc-bsu.cam.ac.uk
%help
CENTER-TBI 6 months GOSe outcome imputation,
cf. https://git.center-tbi.eu/kunzmann/gose-6mo-imputation for details.
%post
apt-get update
apt-get -y install curl python3-pip
pip3 install snakemake
R -e "install.packages('diagram')"
R -e "install.packages('rstan')"
R -e "install.packages('brms')"
R -e "install.packages('mice')"
R -e "install.packages('ggalluvial')"
R -e "install.packages('caret')"
R -e "install.packages('e1071')"
R -e "install.packages('msm')"
R -e "install.packages('cowplot')"
R -e "install.packages('pander')"
R -e "devtools::install_github('kkmann/describr')"
#!/bin/bash
ncpus=$(getconf _NPROCESSORS_ONLN)
snakemake $1 --use-singularity -j $ncpus
#!/bin/bash
# single input: snakemake target
nohup snakemake $1 --use-singularity -j 99 --cluster-config cluster.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -n {cluster.n} -c {threads} -t {cluster.time}" &
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