Zenodo

.gitignore

@@ -3,6 +3,7 @@ output
 .snakemake
 .Rproj.user
 .cache
+container.sif
 *.zip
 *.pdf
 *.Rproj

Snakefile

-singularity: "docker://kkmann/gose-6mo-imputation@sha256:85724229d8f4243aaebd6228e5cc7833474577ac107f9719b00016765f9ee342"
+singularity: "container.sif"
 
 configfile: "config.yml"
 

cluster.json

@@ -2,7 +2,7 @@
     "__default__" :
     {
         "account" :   "MRC-BSU-SL2-CPU",
-        "time" :      "06:00:00",
+        "time" :      "03:00:00",
         "n" :          1,
         "partition" : "bsu-cpu"
     }

docker/build

-#!/bin/bash
-USERNAME="kkmann"
-IMAGE="gose-6mo-imputation"
-BUILDNAME=$USERNAME/$IMAGE
-
-docker build --no-cache -t $BUILDNAME .

docker/dockerfile

-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')"

rules/download.rule

@@ -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"

scripts/download_container.sh

+#!/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

singularity-container-recipe

+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')"

snakemake

-#!/bin/bash
-ncpus=$(getconf _NPROCESSORS_ONLN)
-snakemake $1 --use-singularity -j $ncpus

snakemake_slurm → snakemake_on_slurm_cluster

 #!/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}" &