# Install via PowerShell 
iwr https://cli.formbio.com/public/latest/install/windows | iex

# Install via command line
curl -sSL https://cli.formbio.com/public/latest/install/macos | bash

sudo mkdir -p /usr/local/bin/

# Make it available on your $PATH (only need to do this the first time you install)
sudo ln -s $HOME/.local/bin/formbio /usr/local/bin/formbio

# Install via command line
curl -sSL https://cli.formbio.com/public/latest/install/linux | bash

# Make it available on your $PATH (only need to do this the first time you install)
sudo ln -s $HOME/.local/bin/formbio /usr/local/bin/formbio

# logs the user in 
formbio auth login

# logs the user in when they are already authenticated
formbio auth login

# logs the user out
formbio auth logout

# list currently authenticated user
formbio auth whoami

# list files in top level of project space
formbio storage ls \
   formbio://my-organization/my-project/

# list files recursively in the "logs" directory
formbio storage ls -r \
   formbio://my-organization/my-project/logs/

# download a single file from the project into mylocaldir
formbio storage cp \
  formbio://my-organization/my-project/logs/my_file.txt \
  mylocaldir/

# upload a single file to the project root
formbio storage cp \
  mylocaldir/my_file.txt \
  formbio://my-organization/my-project/

# upload a local directory to a project subdirectory
formbio storage cp -r \
  mylocaldir \
  formbio://my-organization/my-project/subdir/

# resume a partially completed upload
formbio storage cp -c \
  one_gig_file.txt \
  formbio://my-organization/my-project/large-files-dir/

# downloads files that match the wildcard
# workaround for wildcard support which will come soon:
# formbio storage cp formbio://path/*.txt .
formbio storage ls \
  formbio://my-organization/my-project/logs | grep txt |rev| cut -f 1 -d ' ' | rev | awk '{print "formbio storage cp",$1,"."}' |sh

# use the -p (--parents) flag to create several nested directories at once
formbio storage mkdir \
    -p \
    formbio://my-organization/my-project/existing_dir/new_dir/also_new

# For a given Form Bio Org / Project e.g. Org=form-bio-solutions / Project=rna-seq 
# https://form.bio/organizations/form-bio-solutions/projects/rna-seq/home/
# for JSON output, use the --response-format=JSON flag
$ formbio workflow run \
    --env prod \
    --org form-bio-solutions \
    --project rna-seq \
    --repo nf-rnaseq \
    --workflow expressiondetective \
    --version v1.0.0  \
    --run-name 'runRNASEq' \
    -- \
    --design=formbio://form-bio-solutions/rna-seq/SRP045500.design.txt \
    --input=formbio://form-bio-solutions/rna-seq/pipeline-outputs/getncbi/2023-05-06T00_24_44Z_90a32859-6a83-4fec-882d-38df4147a4aa/output/ \
    --genomeid=GRCh38 \
    --genoannotver=latest \
    --version=rnaseq_v1.0.0 \
    --trim=true \
    --cancer=false \
    --aligner=star \
    --repoDir=/seqprg \
    --markdups=skip \
    --stranded=U \
    --readorigin=F \
    --sourceType=cts \
    --orientation=I \
    --genomes_bucket=gs://bioinfo-workflow-references/genomes \
    --taxid=9606

Creating the workflow...
Your run output is available at: 
https://form.bio/organizations/form-bio-solutions/projects/rna-seqUsage:
  formbio workflow run --org org --project project --repo repo --version version --runName runName  -- [--paramName <param-value>] [--paramName2 <param-value>] [flags]

# for JSON output, use the --response-format=JSON flag
$ formbio workflow-run get 9dc2d02a-b8eb-438c-9bb7-2f61fdf5066e

┌───────────────────────────────────────────────────┐
| ID         | 9dc2d02a-b8eb-438c-9bb7-2f61fdf5066e |
| Name       | runRNASEq                            |
| Repository | expressiondetective                  |
| User       | A. N. Nother                         |
| Status     | FAILED                               |
| Created    | 2024-02-29 21:10:56                  |
| Updated    | 2024-02-29 21:15:11                  |
└───────────────────────────────────────────────────┘

# Web links for this workflow run

To view workflow run:
https://formbio.com/organizations/form-bio-solutions/projects/rna-seq/workflow-runs/9dc2d02a-b8eb-438c-9bb7-2f61fdf5066e/

To view workflow run output files in data manager:
(may not work immediately)
https://formbio.com/organizations/form-bio-solutions/projects/rna-seq/vault/?path=pipeline-outputs%2Fexpressiondetective%2F2024-02-29T21_10_56Z_9dc2d02a-b8eb-438c-9bb7-2f61fdf5066e


# CLI commands for this workflow run

To get details about this workflow run:
formbio workflow-run get a9bc9dae-742b-496b-a4b4-4ee4daf9c95b

To list the workflow output directories and files:
(may not work immediately)
formbio storage ls formbio://form-bio-solutions/rna-seq/pipeline-outputs/developerdecoy/2024-02-29T21_10_56Z_a9bc9dae-742b-496b-a4b4-4ee4daf9c95b/