Dockerfile updated

Dockerfile

@@ -1,6 +1,10 @@
-FROM bioconductor/devel_proteomics:latest
-MAINTAINER Tyler Backman <[email protected]>
-RUN printf "source(\"http://bioconductor.org/biocLite.R\")\nbiocLite(c(\"ape\",\"devtools\"))\ndevtools::install_github(\"TylerBackman/bioassayR\")\n" | R --slave
-RUN apt-get update && apt-get install -y hmmer
+FROM bioconductor/bioconductor_docker:latest
+MAINTAINER Tyler Backman <[email protected]>
+# Update Bioconductor packages from devel version
+RUN Rscript --vanilla -e "options(repos = c(CRAN = 'https://cran.r-project.org')); BiocManager::install(ask=FALSE)"
+# Install required Bioconductor packages from devel version
+RUN Rscript -e 'BiocManager::install("bioassayR")'
+RUN Rscript -e 'install.packages("R.utils")'
+RUN apt-get update && apt-get install -y hmmer && apt-get install -y sqlite3
 ADD . /pubchem-bioassay-database
 RUN cd /pubchem-bioassay-database && make working/summarystats.txt

make.sh

@@ -1,14 +1,18 @@
 #!/bin/bash -l
 
-#PBS -j oe
-#PBS -l walltime=100:00:00
-#PBS -l nodes=1:ppn=8
-#PBS -l mem=8gb
-##PBS -q highmem
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=10
+#SBATCH --mem=10G
+#SBATCH --time=1-00:15:00     # 1 day and 15 minutes
+#SBATCH [email protected]
+#SBATCH --mail-type=ALL
+#SBATCH --job-name="database"
+#SBATCH -p intel # This is the default partition, you can use any of the following; intel, batch, highmem, gpu
 
 cd $PBS_O_WORKDIR
 
 export cores="$PBS_NP"
-module load R/3.2.2 
-module load hmmer/3.1b2
+module load R/4.1.0_gcc-8.3.0
+module load hmmer/3.3.2
 make -e working/summarystats.txt

src/buildBioassayDatabase.R

@@ -11,7 +11,7 @@ targetType <- commandArgs(trailingOnly=TRUE)[2]
 outputDatabase <- commandArgs(trailingOnly=TRUE)[3]
 
 # test code for running without make:
-if(is.na(commandArgs(trailingOnly=TRUE)[1])){
+if(is.null(commandArgs(trailingOnly=TRUE)[1])){
 	bioassayMirror <- "working/bioassayMirror"
     targetType <- "proteinsOnly"
 	outputDatabase <- "working/bioassayDatabase.sqlite"