-
Similar CLI: Caper has a similar CLI as Cromwell.
-
Built-in backends: You don't need your own backend configuration file. Caper provides built-in backends.
-
Automatic transfer between local/cloud storages: You can use URIs (e.g.
gs://
,http(s)://
ands3://
) instead of paths in a command line arguments, also in your input JSON file. Files associated with these URIs will be automatically transfered to a specified temporary directory on a target remote storage. -
Deepcopy for input JSON file: Recursively copy all data files in (
.json
,.tsv
and.csv
) to a target remote storage. It's activate by default. Use--no-deepcopy
to disable this feature. -
Docker/Singularity integration: You can run a WDL workflow in a specifed docker/singularity container.
-
MySQL database integration: Caper provide shell scripts to run a MySQL database server in a docker/singularity container. Using Caper with those databases will allow you to use Cromwell's call-caching to re-use outputs from previous successful tasks. This will be useful to resume a failed workflow where it left off.
-
One configuration file for all: You may not want to repeat writing same command line parameters for every pipeline run. Define parameters in a configuration file at
~/.caper/default.conf
. -
One server for six backends: Built-in backends allow you to submit pipelines to any local/remote backend specified with
-b
or--backend
. -
Cluster engine support: SLURM, SGE and PBS are currently supported locally.
-
Easy workflow management: Find all workflows submitted to a Cromwell server by workflow IDs (UUIDs) or
str_label
(special label for a workflow submitted by Capersubmit
andrun
). You can define multiple keywords with wildcards (*
and?
) to search for matching workflows. Abort, release hold, retrieve metadata JSON for them. -
Automatic subworkflow packing: Caper automatically creates an archive (
imports.zip
) of all imports and send it to Cromwell server/run. -
Special label (
str_label
): You have a string label, specified with-s
or--str-label
, for your workflow so that you can search for your workflow by this label instead of Cromwell's workflow UUID (e.g.f12526cb-7ed8-4bfa-8e2e-a463e94a61d0
).
There are 7 subcommands available for Caper. Except for run
other subcommands work with a running Caper server, which can be started with server
subcommand. server
does not require a positional argument. WF_ID
(workflow ID) is a UUID generated from Cromwell to identify a workflow. STR_LABEL
is Caper's special string label to be used to identify a workflow.
Subcommand | Positional args | Description |
---|---|---|
init | PLATFORM | Generate a default configuration file for a specified PLATFORM |
server | Run a Cromwell server with built-in backends | |
run | WDL | Run a single workflow (not recommened for multiple workflows) |
submit | WDL | Submit a workflow to a Cromwell server |
abort | WF_ID or STR_LABEL | Abort submitted workflows on a Cromwell server |
unhold | WF_ID or STR_LABEL | Release hold of workflows on a Cromwell server |
list | WF_ID or STR_LABEL | List submitted workflows on a Cromwell server |
metadata | WF_ID or STR_LABEL | Retrieve metadata JSONs for workflows |
debug, troubleshoot | WF_ID, STR_LABEL or METADATA_JSON_FILE |
Analyze reason for errors |
-
init
: To initialize Caper on a given platform. This command also downloads Cromwell/Womtool JARs so that Caper can work completely offline with local data files.Platform Description sherlock Stanford Sherlock cluster (SLURM) scg Stanford SCG cluster (SLURM) gcp Google Cloud Platform aws Amazon Web Service local General local computer sge HPC with Sun GridEngine cluster engine pbs HPC with PBS cluster engine slurm HPC with SLURM cluster engine -
run
: To run a single workflow. A string label-s
is optional and useful for other subcommands to indentify a workflow.$ caper run [WDL] -i [INPUT_JSON]
WARNING: If you use a file DB (
--file-db
) and try to run multiple workflows at the same time then you will see adb - Connection is not available
error message since multiple Caper instances will try to lock the same DB file~/.caper/default_file_db
.java.sql.SQLTransientConnectionException: db - Connection is not available, request timed out after 3000ms.
WORKAROUND: Define a different DB file per run with
--file-db
. Or start a caper server and submit multiple workflows to it so that the DB file is taken by one caper server only. Or use a server-based MySQL database instead. -
server
: To start a server. You can define a server port with--port
. Use a different port for each server for multiple servers. If you don't use a default port (8000
). Then define--port
for all client subcommands likesubmit
,list
andtroubleshoot
. If you run a server on a different IP address or hostname, then define it with--ip
for all client subcomands likesubmit
.$ caper server
-
submit
: To submit a workflow to a server. Define a string label for submitted workflow with-s
. It is optional but useful for other subcommands to indentify a workflow.$ caper submit [WDL] -i [INPUT_JSON] -s [STR_LABEL]
-
list
: To show a list of all workflows submitted to a cromwell server. Wildcard search with using*
and?
is allowed for such label for the following subcommands withSTR_LABEL
.$ caper list [WF_ID or STR_LABEL]
-
debug
ortroubleshoot
: To analyze reasons for workflow failures. You can specify failed workflow's metadata JSON file or workflow IDs and labels. Wildcard search with using*
and?
is allowed for string labels.$ caper debug [WF_ID, STR_LABEL or METADATA_JSON_FILE]
-
Other subcommands: Other subcommands work similar to
list
. It does a corresponding action for matched workflows.
IMPORTANT:
--deepcopy
has been deprecated and it's activated by default. You can disable it with--no-deepcopy
.
Deepcopy allows Caper to RECURSIVELY copy files defined in your input JSON into your target backend's temporary storage. For example, Cromwell cannot read directly from URLs in an input JSON file, but Caper makes copies of these URLs on your backend's temporary directory (e.g. --local-loc-dir
for local
, --gcp-loc-dir
for gcp
) and pass them to Cromwell.
It is useful to have a configuration file per project. For example of two projects.
We want to run pipelines locally for project-1, run a server with caper -c project_1.conf server
and submit a workflow with caper -c project_1.conf submit [WDL] ...
or run a single workflow caper -c project_1.conf run [WDL] ...
.
db=file
file-db=~/.caper/file_db_project_1
port=8000
backend=local
local-out-dir=/scratch/user/caper_out_project_1
We want to run pipelines on Google Cloud Platform for project-2. Run a server with caper -c project_2.conf server
and submit a workflow with caper -c project_2.conf submit [WDL] ...
or run a single workflow caper -c project_2.conf run [WDL] ...
.
db=file
file-db=~/.caper/file_db_project_2
port=8001
backend=gcp
gcp-prj=YOUR_GCP_PRJ_NAME
gcp-out-dir=gs://caper_out_project_2
Then you will see no conflict in file DBs and network ports (8000
vs. 8001
) between two projects.
We highly recommend to use a default configuration file described in the section Configuration file. Note that both dash (-
) and underscore (_
) are allowed for key names in a configuration file.
-
Basic parameters that are similar to Cromwell.
Cmd. line Description --inputs, -i Workflow inputs JSON file --options, -o Workflow options JSON file --labels, -l Workflow labels JSON file --imports, -p Zip file of imported subworkflows --metadata-output, -m Path for output metadata JSON file (for run
mode only) -
Caper's special parameters. You can define a docker/singularity image to run your workflow with.
Cmd. line Description --dry-run Caper generates all temporary files but does not take any action. --str-label, -s Caper's special label for a workflow. This will be used to identify a workflow submitted by Caper --docker Docker image URI for a WDL. You can also use this as a flag. You can also use this as a flag to use Docker image defined in your WDL as a special comment #CAPER docker [IMAGE]
.--singularity Singularity image URI for a WDL. You can also use this as a flag to use Singularity image defined in your WDL as a special comment #CAPER singularity [IMAGE]
.--no-build-singularity Local singularity image will not be built before running/submitting a workflow --singularity-cachedir Singularity image URI for a WDL --db Metadata DB type (file: not recommended, mysql: recommended, in-memory: no metadata DB) --file-db, -d File-based metadata DB for Cromwell's built-in HyperSQL database (UNSTABLE) --db-timeout Milliseconds to wait for DB connection (default: 30000) --java-heap-server Java heap memory for caper server (default: 10G) --disable-auto-write-metadata Disable auto update/retrieval/writing of metadata.json
on workflow's output directory.--java-heap-run Java heap memory for caper run (default: 3G) --show-subworkflow Include subworkflow in caper list
search query. WARNING: If there are too many subworkflows, then you will see HTTP 503 error (service unavaiable) or Caper/Cromwell server can crash. -
Choose a default backend. Deepcopy is enabled by default. All data files will be automatically transferred to a target local/remote storage corresponding to a chosen backend. Make sure that you correctly configure temporary directories for source/target storages (
--local-loc-dir
,--gcp-loc-dir
and--aws-loc-dir
). To disable this feature use--no-deepcopy
.Conf. file Cmd. line Default Description backend -b, --backend local Caper's built-in backend to run a workflow. Supported backends: local
,gcp
,aws
,slurm
,sge
andpbs
. Make sure to configure for chosen backendhold --hold Put a hold on a workflow when submitted to a Cromwell server no-deepcopy --no-deepcopy Disable deepcopy (copying files defined in an input JSON to corresponding file local/remote storage) format --format, -f id,status,
name,
str_label,
submissionComma-separated list of items to be shown for list
subcommand. Supported formats:id
(workflow UUID),status
,name
(WDL basename),str\_label
(Caper's special string label),parent
(parent's workflow UUID:None
if not subworkflow),submission
,start
,end
hide-result-before --hide-result-before Datetime string to hide old workflows submitted before it. This is based on a simple string comparison (sorting). (e.g. 2019-06-13, 2019-06-13T10:07) -
Special parameter for a direct transfer between S3 and GCS buckets
Conf. file Cmd. line Default Description use-gsutil-for-s3 --use-gsutil-for-s3 Use gsutil
for direct transfer between S3 and GCS buckets. Otherwise Caper streams file transfer through local machine for S3 <-> GCS. Make sure thatgsutil
is installed and authentication for both GCS and S3 is done on shell environment level. -
Local backend settings
Conf. file Cmd. line Default Description local-out-dir, out-dir --local-out-dir, --out-dir $CWD
Output directory for local backend local-loc-dir, tmp-dir --local-loc-dir, --tmp-dir $CWD/caper\_tmp
Tmp. directory for localization on local backend -
Google Cloud Platform backend settings
Conf. file Cmd. line Description gcp-prj --gcp-prj Google Cloud project use-google-cloud-life-sciences --use-google-cloud-life-sciences Use Google Cloud Life Sciences API instead of (deprecated) Genomics API gcp-memory-retry-error-keys --gcp-memory-retry-error-keys If an error caught by these comma-separated keys occurs then increase instance's memory by --gcp-memory-retry-multiplier and retry (controlled by --max-retries). gcp-memory-retry-multiplier --gcp-memory-retry-multiplier Multiplier for memory-retry. gcp-zones --gcp-zones Comma-delimited Google Cloud Platform zones to provision worker instances (e.g. us-central1-c,us-west1-b) gcp-out-dir, out-gcs-bucket --gcp-out-dir, --out-gcs-bucket Output gs://
directory for GC backendgcp-loc-dir, tmp-gcs-bucket --gcp-loc-dir, --tmp-gcs-bucket Tmp. directory for localization on GC backend -
AWS backend settings
Conf. file Cmd. line Description aws-batch-arn --aws-batch-arn ARN for AWS Batch aws-region --aws-region AWS region (e.g. us-west-1) aws-out-dir, out-s3-bucket --aws-out-dir, --out-s3-bucket Output s3://
directory for AWS backendaws-loc-dir, tmp-s3-bucket --aws-loc-dir, --tmp-s3-bucket Tmp. directopy for localization on AWS backend DEPREACTED OLD PARAMETERS:
Conf. file Cmd. line Description use-gsutil-over-aws-s3 --use-gsutil-over-aws-s3 DEPREACTED. -
Private URLs settings Caper defaults to use
~/.netrc
file to get access to private URLs. This is useful, particularly for ENCODE portal, for using private URLs (http(s)://
) directly in your input JSON.DEPREACTED OLD PARAMETERS.
Conf. file Cmd. line Description http-user --http-user DEPRECATED http-password --http-password DEPRECATED use-netrc --use-netrc DEPRECATED -
MySQL settings. Run a MySQL server with shell scripts we provide and make Cromwell server connect to it instead of using its in-memory database. This is useful when you need to re-use outputs from previous failed workflows when you resume them.
Conf. file Cmd. line Default Description mysql-db-ip --mysql-db-ip localhost (Optional) MySQL DB IP address mysql-db-port --mysql-db-port 3306 MySQL DB port mysql-db-user --mysql-db-user cromwell (Optional) MySQL DB username mysql-db-password --mysql-db-password cromwell (Optional) MySQL DB password mysql-db-name --mysql-db-name cromwell (Optional) MySQL DB name for Cromwell -
PostgreSQL settings.
Conf. file Cmd. line Default Description postgresql-db-ip --postgresql-db-ip localhost (Optional) PostgreSQL DB IP address postgresql-db-port --postgresql-db-port 3306 PostgreSQL DB port postgresql-db-user --postgresql-db-user cromwell (Optional) PostgreSQL DB username postgresql-db-password --postgresql-db-password cromwell (Optional) PostgreSQL DB password postgresql-db-name --postgresql-db-name cromwell (Optional) PostgreSQL DB name for Cromwell -
Caper server/run parameters.
Conf. file Cmd. line Default Description cromwell --cromwell cromwell-52.jar Path or URL for Cromwell JAR file max-concurrent-tasks --max-concurrent-tasks 1000 Maximum number of concurrent tasks max-concurrent-workflows --max-concurrent-workflows 40 Maximum number of concurrent workflows max-retries --max-retries 1 Maximum number of retries for failing tasks disable-call-caching --disable-call-caching Disable Cromwell's call-caching (re-using outputs) soft-glob-output --soft-glob-output Use soft-linking for globbing outputs for a filesystem that does not allow hard-linking: e.g. beeGFS. backend-file --backend-file Custom Cromwell backend conf file. This will override Caper's built-in backends -
Caper server/client parameters.
Conf. file Cmd. line Default Description ip --ip localhost Cromwell server hostname/IP address or hostname port --port 8000 Cromwell server port no-server-heartbeat --no-server-heartbeat Flag to disable server heartbeat file. server-heartbeat-file --server-heartbeat-file ~/.caper/default_server_heartbeat
Heartbeat file for Caper clients to get IP and port of a server. -
Caper run/client parameters.
Conf. file Cmd. line Default Description womtool --womtool womtool-51.jar Path or URL for Womtool JAR file (to validate WDL/inputs). ignore-womtool --ignore-womtool False Skip Womtool validation. java-heap-womtool --java-heap-womtool 1G Java heap memory for Womtool. -
Caper client parameters.
Conf. file Cmd. line Default Description server-heartbeat-timeout --server-heartbeat-timeout 120000 Timeout for a heartbeat file in Milliseconds. -
Troubleshoot parameters for
caper troubleshoot
subcommand.Cmd. line Description --show-completed-task Show completed tasks when troubleshooting -
SLURM backend settings. This is useful for Stanford Clusters (Sherlock, SCG). Define
--slurm-partition
for Sherlock and--slurm-account
for SCG.Conf. file Cmd. line Description slurm-partition --slurm-partition SLURM partition slurm-account --slurm-account SLURM account slurm-extra-param --slurm-extra-param Extra parameters for SLURM sbatch
command -
SGE backend settings. Make sure to have a parallel environment configured on your system. Ask your admin to add it if not exists.
Conf. file Cmd. line Description sge-pe --sge-pe SGE parallel environment. Check with qconf -spl
sge-queue --sge-queue SGE queue to submit tasks. Check with qconf -sql
slurm-extra-param --slurm-extra-param Extra parameters for SGE qsub
command -
PBS backend settings.
Conf. file Cmd. line Description pbs-queue --pbs-queue PBS queue to submit tasks. pbs-extra-param --pbs-extra-param Extra parameters for PBS qsub
command
We highly recommend to use a default configuration file explained in the section Configuration file.
There are six built-in backends for Caper. Each backend must run on its designated storage. To use cloud backends (gcp
and aws
) and corresponding cloud storages (gcs
and s3
), you must install cloud platform's CLIs (gsutil
and aws
). You also need to configure these CLIs for authentication. See configuration instructions for GCP and AWS for details. Define required parameters in command line arguments or in a configuration file.
Backend | Description | Storage | Required parameters |
---|---|---|---|
gcp | Google Cloud Platform | gcs | --gcp-prj, --gcp-out-dir, --gcp-loc-dir |
aws | AWS | s3 | --aws-batch-arn, --aws-region, --aws-out-dir, --aws-loc-dir |
Local | Default local backend | local | --local-out-dir, --local-loc-dir |
slurm | local SLURM backend | local | --local-out-dir, --local-loc-dir, --slurm-partition or --slurm-account |
sge | local SGE backend | local | --local-out-dir, --local-loc-dir, --sge-pe |
pds | local PBS backend | local | --local-out-dir, --local-loc-dir |
You can also use your own MySQL database if you configure MySQL for Caper.
Caper supports Singularity for its local built-in backend (local
, slurm
, sge
and pbs
). Tasks in a workflow will run inside a container and outputs will be pulled out to a host from it at the end of each task. You need to add --singularity
to use your own Singularity image. SINGULARITY_IMAGE_URI
is OPTIONAL. You can omit it then Caper will try to find a Singularity image URI defined in your WDL as a comment.
$ caper run [WDL] -i [INPUT_JSON] --singularity [SINGULARITY_IMAGE_URI_OR_LEAVE_IT_BLANK]
Define a cache directory where local Singularity images will be built. You can also define an environment variable SINGULARITY_CACHEDIR
.
singularity-cachedir=[SINGULARITY_CACHEDIR]
Singularity image will be built first before running a workflow to prevent mutiple tasks from competing to write on the same local image file. If you don't define it, every task in a workflow will try to repeatedly build a local Singularity image on their temporary directory.
Caper supports Docker for its non-HPC backends (local
, aws
and gcp
).
WARNING: For
aws
andgcp
backends Caper will try to find a Docker image URI defined in your WDL as a comment even if--docker
is not explicitly defined.
Tasks in a workflow will run inside a container and outputs will be pulled out to a host from it at the end of each task. DOCKER_IMAGE_URI
is OPTIONAL. If it's not defined then Caper will try to find a Docker image URI defined in your WDL as a comment.
$ caper run [WDL] -i [INPUT_JSON] --docker [DOCKER_IMAGE_URI_OR_LEAVE_IT_BLANK]
Activate your CONDA_ENV
before running Caper (both for run
and server
modes).
$ conda activate [COND_ENV]
There are four types of storages. Each storage except for URL has its own working/temporary directory/uri defined by the following parameters. These directories are used for storing Caper's intermediate files and cached big data files for localization on corrsponding storages. e.g. localizing files on GCS to S3 (on --gcp-loc-dir) to run pipeline on AWS instance with GCS files.
Storage | URI(s) | Command line parameter |
---|---|---|
local | Path | --local-loc-dir |
gcs | gs:// | --gcp-loc-dir |
s3 | s3:// | --aws-loc-dir |
url | http(s):// | not available (read-only) |
Output directories are defined similarly as temporary ones. Those are actual output directories (called cromwell_root
, which is cromwell-executions/
by default) where Cromwell's output are actually written to.
Storage | URI(s) | Command line parameter |
---|---|---|
local | Path | --local-out-dir |
gcs | gs:// | --gcp-out-dir |
s3 | s3:// | --aws-out-dir |
url | http(s):// | not available (read-only) |
Workflow's final output file metadata.json
will be written to each workflow's directory (with workflow UUID) under this output directory.
Inter-storage transfer is done by keeping source's directory structure and appending to target storage temporary directory. For example of the following temporary directory settings for each backend,
Storage | Command line parameters |
---|---|
local | --local-loc-dir /scratch/user/caper_tmp |
gcs | --gcp-loc-dir gs://my_gcs_bucket/caper_tmp |
s3 | --aws-loc-dir s3://my_s3_bucket/caper_tmp |
A local file /home/user/a/b/c/hello.gz
can be copied (on demand) to
Storage | Command line parameters |
---|---|
gcs | gs://my_gcs_bucket/caper_tmp/home/user/a/b/c/hello.gz |
s3 | s3://my_s3_bucket/caper_tmp/home/user/a/b/c/hello.gz |
File transfer is done by using the following command lines using various CLIs:
gsutil -q cp -n [SRC] [TARGET]
aws s3 cp --only-show-errors [SRC] [TARGET]
curl -RL -f -C - [URL_SRC] -o [TARGET]
curl -RL -f [URL_SRC] | gsutil -q cp -n - [TARGET]
WARNING: Caper does not ensure a fail-safe file transfer when it's interrupted by user or system. Also, there can be race conditions if multiple users try to access/copy files. This will be later addressed in the future release. Until then DO NOT interrupt file transfer until you see the following
copying done
message.
Example:
[CaperURI] copying from gcs to local, src: gs://encode-pipeline-test-runs/test_wdl_imports/main.wdl
[CaperURI] copying done, target: /srv/scratch/leepc12/caper_tmp_dir/encode-pipeline-test-runs/test_wdl_imports/main.wdl
WARNING: Please keep your local temporary directory SECURE. Caper writes temporary files (
backend.conf
,inputs.json
,workflow_opts.json
andlabels.json
) for Cromwell onlocal
temporary directory defined by--local-loc-dir
. The following sensitive information can be exposed on these directories.
Sensitve information | Temporary filename |
---|---|
MySQL database username | backend.conf |
MySQL database password | backend.conf |
PostgreSQL database username | backend.conf |
PostgreSQL database password | backend.conf |
AWS Batch ARN | backend.conf |
Google Cloud Platform project name | backend.conf |
SLURM account name | workflow_opts.json |
SLURM partition name | workflow_opts.json` |
WARNING: Also, please keep other temporary directories SECURE too. Your data files defined in your input JSON file can be recursively transferred to any of these temporary directories according to your target backend defined by
-b
or--backend
.
Optional: Add the following comments to your WDL then Caper will be able to find an appropriate container image for your WDL. Then you don't have to define them in command line arguments everytime you run a pipeline.
#CAPER singularity [SINGULARITY_IMAGE_URI: e.g. docker://ubuntu:latest or shub://SUI-HPC/mysql]
#CAPER docker [DOCKER_IMAGE_URI: e.g. ubuntu:latest]