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Docker is a great tool to ensure reproducibility of your computing work. I was
using the bioconductor image on google cloud, but the image does not have the gsutil command.
You can install once in the container, but once you exit the container, the gsutil command will be gone. You will need to modify the docker image if you want to keep using it.
Step 1
$ sudo docker images -a
REPOSITORY TAG IMAGE ID CREATED SIZE
rocker/tidyverse latest d4d41e410fb7 2 months ago 2.16GB
r-base latest 3de1ef2039fb 3 months ago 838MB
bioconductor/bioconductor_docker RELEASE_3_15 75cc0e27e8ea 6 months ago 4.23GB
hello-world latest feb5d9fea6a5 17 months ago 13.3kB
Step 2
run the bioconductor/bioconductor_docker docker container interactively in bash:
$ sudo docker run -it 75cc0e27e8ea bin/bash
Step 3
Modify the container by installing gsutils
$ gsutil
bash: gsutil: command not found
$ curl -sSL https://sdk.cloud.google.com | bash
Performing post processing steps...done.
Update done!
Modify profile to update your $PATH and enable shell command completion?
Do you want to continue (Y/n)?
It will add the gsutil to your PATH. Exit the container:
$ exit
Step 4
Find the container ID:
$ sudo docker ps -a | head
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
ab9c4b13c67c bioconductor/bioconductor_docker:RELEASE_3_15 "/init" 36 seconds ago Up 35 seconds 0.0.0.0:8787->8787/tcp, :::8787->8787/tcp keen_khayyam
d3786b7b53a5 75cc0e27e8ea "bin/bash" 10 minutes ago Exited (127) 23 seconds ago quirky_cori
d6a94d025154 bioconductor/bioconductor_docker:RELEASE_3_15 "/init" About an hour ago Exited (0) About a minute ago kind_goldwasser
ab7e03d1d665 bioconductor/bioconductor_docker:RELEASE_3_15 "/init" About an hour ago Exited (0) About an hour ago wonderful_bouman
sudo docker commit [CONTAINER_ID] [new_image_name] to commit the changes:
$ sudo docker commit d3786b7b53a5 bioconductor_gstuils
Step 5
Hoary! The bioconductor_gstuils image is created!
$ sudo docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
bioconductor_gstuils latest 375c7ec8354f 2 minutes ago 5.49GB
rocker/tidyverse latest d4d41e410fb7 2 months ago 2.16GB
r-base latest 3de1ef2039fb 3 months ago 838MB
bioconductor/bioconductor_docker RELEASE_3_15 75cc0e27e8ea 6 months ago 4.23GB
hello-world latest feb5d9fea6a5 17 months ago 13.3kB
The gsutil command is now avaiable in the new docker container.
$ sudo docker run -it bioconductor_gstuils bin/bash
$ gsutil
Usage: gsutil [-D] [-DD] [-h header]... [-i service_account] [-m] [-o section:flag=value]... [-q] [-u user_project] [command [opts...] args...]
Available commands:
acl Get, set, or change bucket and/or object ACLs
autoclass Configure Autoclass feature
bucketpolicyonly Configure uniform bucket-level access
cat Concatenate object content to stdout
compose Concatenate a sequence of objects into a new composite object.
config Obtain credentials and create configuration file
cors Get or set a CORS JSON document for one or more buckets
cp Copy files and objects
defacl Get, set, or change default ACL on buckets
defstorageclass Get or set the default storage class on buckets
du Display object size usage
hash Calculate file hashes
help Get help about commands and topics
hmac CRUD operations on service account HMAC keys.
iam Get, set, or change bucket and/or object IAM permissions.
kms Configure Cloud KMS encryption
label Get, set, or change the label configuration of a bucket.
lifecycle Get or set lifecycle configuration for a bucket
logging Configure or retrieve logging on buckets
ls List providers, buckets, or objects
mb Make buckets
mv Move/rename objects
notification Configure object change notification
pap Configure public access prevention
perfdiag Run performance diagnostic
rb Remove buckets
requesterpays Enable or disable requester pays for one or more buckets
retention Provides utilities to interact with Retention Policy feature.
rewrite Rewrite objects
rm Remove objects
rpo Configure replication
rsync Synchronize content of two buckets/directories
setmeta Set metadata on already uploaded objects
signurl Create a signed URL
stat Display object status
test Run gsutil unit/integration tests (for developers)
ubla Configure Uniform bucket-level access
update Update to the latest gsutil release
version Print version info about gsutil
versioning Enable or suspend versioning for one or more buckets
web Set a website configuration for a bucket
...
Use gsutil help <command or topic> for detailed help.
Hmm.. but now the below command does not bring up the Rstudio.
sudo docker run \
-v /home/tommytang:/home/rstudio/tommytang \
-v /home/tommytang/R/host-site-library:/usr/local/lib/R/host-site-library \
-e R_LIBS_USER=/home/tommytang/R/host-site-library \
-p 8787:8787 \
bioconductor_gstuils
What’s wrong?
I know I can also add RUN curl -sSL https://sdk.cloud.google.com | bash to the bioconductor docker file and
build a new docker image. That probably will work.