- this package was originally hosted at https://github.com/Benjamin-Vincent-Lab/rserver-binfotron and was moved here on 2/13/2024
This Dockerfile is used to run binfotron functions.
https://hub.docker.com/repository/docker/benjaminvincentlab/rserver-binfotron
docker build -t benjaminvincentlab/rserver-binfotron:4.4.1.05 .docker run -e PASSWORD=12qwaszx --rm -p 8787:8787 -v ~/Desktop:/home/rstudio benjaminvincentlab/rserver-binfotron:4.4.1.05Then direct browser to localhost:8787. Your username is rstudio.
docker login
docker push benjaminvincentlab/rserver-binfotron:4.4.1.05sbatch -c 4 --mem 8g -p allnodes --wrap="apptainer pull docker://benjaminvincentlab/rserver-binfotron:4.4.1.05"
mv ${APPTAINER_PULLFOLDER}/rserver-binfotron_4.4.1.05.sif /datastore/nextgenout5/share/labs/Vincent_Lab/tools/raft/imgs/benjaminvincentlab-rserver-binfotron-4.4.1.05.img
Either make sure you do all of the following:
- Use the --pid flag. This makes sure the job kills all of the rserver's processes when the job ends. If you don't use this flag, your processess will be left running on the cluster and the next person who uses that node won't be able to change from your bindings.
- Use an open port
- Use a unique '--server-data-dir'
data_dir=$(mktemp -d -t rserver-XXXXXXXX)}
- Make a '--database-config-file'
database_config_path=${data_dir}/database.conf
echo "provider=sqlite" > $database_config_path
echo "directory=${data_dir}" >> $database_config_path
echo "provider=postgresql" >> $database_config_path
echo "host=localhost" >> $database_config_path
echo "database=rstudio" >> $database_config_path
echo "port=5432" >> $database_config_path
echo "username=postgres" >> $database_config_path
echo "password=postgres" >> $database_config_path
echo "connection-timeout-seconds=10" >> $database_config_path
echo "connection-uri=postgresql://postgres@localhost:5432/rstudio?sslmode=allow&options=-csearch_path=public" >> $database_config_path
- Then run
singularity exec --pid --nohttps --home $rstudio_home_dir --bind $bindings $image_path \
rserver --www-port $source_command --server-data-dir $data_dir --database-config-file $database_config_path"
- or -
Use run_rserver to run it. It will do all of the above steps for you.
v.w.x.y
vwx is the version of R.
y is the version of this Dockerfile padded with zeros to 2 digits (eg 4.4.1.05)
cd /home/dbortone/docker/rserver_binfotron
my_comment="Added inflection and kneer. Updated housekeeping, datasetprep, and binfotron "
git commit -am "$my_comment"; git push
my_tag="4.4.1.05"
git tag -a "$my_tag" -m "$my_comment"; git push origin "$my_tag"You should merge with that R version's branch and, if it's the most recent version of R, merge with master.
my_version=4.4.1.05
docker build -t benjaminvincentlab/rserver-binfotron:$my_version .
docker push benjaminvincentlab/rserver-binfotron:$my_version