Welcome to Parsec’s documentation!¶
Contents:
Parsec: Galaxy at the Speed of Light¶
Command-line utilities to assist in working with Galaxy servers.
Installation¶
$ pip install galaxy-parsec
$ parsec init
Questions?¶
Quick Start¶
This quick start demonstrates using parsec commands to manipulate Galaxy
histories and datasets. You will want to install jq
if you do not have it already.
Connect to a Galaxy server¶
To connect to a running Galaxy server, you will need an account on that Galaxy instance and an API key for the account. Instructions on getting an API key can be found at http://wiki.galaxyproject.org/Learn/API .
First initialize parsec:
$ parsec init
Once initialized, parsec will be usable from the command line. Please note that an admin account is required for a few actions like creation of data libraries, or access to user API keys. Your configuration must allow access to /api without need for a username or password. More infomration can be found at https://galaxyproject.org/admin/config/performance/production-server/
Introduction To Parsec¶
Parsec is a set of automatically generated wrappers for BioBlend functions. I found myself writing a large number of small / one-off scripts that invoked simple bioblend functions. These scripts were impossible to compose and use in a linux-friendly manner. I copied and pasted code between all of these utility scripts.
Parsec is the answer to all of these problems. It extracts all of the individual functions I was writing as separate CLI commands that can be piped together, run in parallel, etc.
After installation, running parsec will present you with a list of sub-commands you can execute.
$ parsec
Usage: parsec [OPTIONS] COMMAND [ARGS]...
Command line wrappers around BioBlend functions. While this sounds
unexciting, with parsec and jq you can easily build powerful command line
scripts.
Options:
--version Show the version and exit.
-v, --verbose Enables verbose mode.
--galaxy_instance TEXT name of galaxy instance from ~/.planemo.yml
[required]
--help Show this message and exit.
Commands:
config
datasets
datatypes
folders
forms
...
Each of these commands has more commands under it:
$ parsec histories
Usage: parsec histories [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
Commands:
create_dataset_collection Create a new dataset collection
create_history Create a new history, optionally setting
the...
create_history_tag Create history tag
delete_dataset Mark corresponding dataset as deleted.
delete_dataset_collection Mark corresponding dataset collection as...
delete_history Delete a history.
download_dataset Deprecated method, use...
download_history Download a history export archive.
export_history Start a job to create an export archive
for...
...
Viewing Histories and Datasets¶
To get information on the Histories currently in your account, call history
get_histories, and we will pipe this to a jq command which selects the
first element from the JSON array.
$ parsec histories get_histories | jq '.[0]'
Parsec will respond with information about your first history
{
"name": "BuildID=Manual-2017.05.02T16:13 WF=PAP_2017_Comparative_(v1.0)_BOOTSTRAPPED Org=CCS Source=Jenkins",
"url": "/galaxy/api/histories/548c0777ac615645",
"annotation": null,
"model_class": "History",
"id": "548c0777ac615645",
"tags": [
"Automated",
"Annotation",
"BICH464"
],
"purged": false,
"published": false,
"deleted": false
}
This may not be all of the information you were expecting about your history.
In that case, you might want to call show_history which will show you more
details about a single history. You can either manually type parsec histories
show_history 548c0777ac615645, or we can do this in batch:
$ parsec histories get_histories | jq '.[0].id' | xargs -n 1 parsec histories show_history
Which pulls out the first history, select the id attribute, before passing it to xargs.
If you have not used it before, xargs allows us to execute multiple
commands for some input data. Here we execute the command parsec histories
show_history for each line of input (i.e. each ID returned to us from the jq call).
xargs -n 1 ensures that we will only pass a single ID to a
single call of show_history. If you were to use jq '.[].id' instead of
jq '.[0].id' it would output the IDs for every history you own. You could
then pipe this to xargs and run show_history on all of your histories!
{
"annotation": null,
"contents_url": "/galaxy/api/histories/548c0777ac615645/contents",
"create_time": "2017-05-02T16:18:21.285382",
"deleted": false,
"empty": false,
"genome_build": null,
"id": "548c0777ac615645",
"importable": true,
"model_class": "History",
"name": "BuildID=Manual-2017.05.02T16:13 WF=PAP_2017_Comparative_(v1.0)_BOOTSTRAPPED Org=CCS Source=Jenkins",
"published": false,
"purged": false,
"size": 34760258,
"slug": "buildidmanual-20170502t1613-wfpap2017comparativev10bootstrapped-orgccs-sourcejenkins",
"state": "ok",
"state_details": {
"discarded": 0,
"empty": 0,
"error": 0,
"failed_metadata": 0,
"new": 0,
"ok": 29,
"paused": 0,
"queued": 0,
"running": 0,
"setting_metadata": 0,
"upload": 0
},
"state_ids": {
"discarded": [
"a6cc986453fae8ba",
"f2f9b7b017f20578",
"70eb5af78c588bd1"
],
"empty": [],
"error": [
"d643e34e1114cc52",
"98ae3d35d73f82c9"
],
"failed_metadata": [],
"new": [],
"ok": [
"e510305efbee5f49",
"0d595b7c2b6e9b93",
"d04ac6f949ae266c",
"175f283ddaeca39c",
"b34432b8a0847c04",
"ea7ff5323ddebcb8",
"3e40a393efafc45c",
"7ce5ec5d51ef85cb",
"577e4242cdfbe1aa",
"193d15527d13f45e",
"4543f9456af7f0df",
"5e1293df75b4f95b",
"a57bae35eca5fbfe",
"6c306b2ed4533f1f",
"97c5f81b159505f0",
"64d1d8e46b4554bd",
"8e9432496d7e2b43",
"5c8579257c579aae",
"243ad216fbfa268e",
"8336d9eb27b27677",
"a1d4cc61bdba629d",
"7f93a80890822fa9",
"c479b351902302e2",
"36b60fb58ad24a71",
"041dd3cb6879f1f7",
"36992e90715c9c77",
"4bddfe152467e972",
"2d9f5c0c36d89e10",
"e53ad6f3133b2816"
],
"paused": [
"4a8143557292a233",
"b0f8a75aa6be2c1d"
],
"queued": [],
"running": [],
"setting_metadata": [],
"upload": []
},
"tags": [
"Automated",
"Annotation",
"BICH464"
],
"update_time": "2017-05-02T16:49:07.941097",
"url": "/galaxy/api/histories/548c0777ac615645",
"user_id": "f570ade6e7840ba0",
"username_and_slug": "u/helena-rasche/h/buildidmanual-20170502t1613-wfpap2017comparativev10bootstrapped-orgccs-sourcejenkins"
}
So much metadata to play with and filter on! Note that many of these commands
have additional flags, for example parsec histories show_history --help
will tell us that we can also pass the –contents option to retrieve a list of datasets in that history, even filtering on their visibility.
$ parsec histories show_history --help
Usage: parsec histories show_history [OPTIONS] HISTORY_ID
Get details of a given history. By default, just get the history meta
information.
Options:
--contents When ``True``, the complete list of datasets in the given
history.
--deleted TEXT Used when contents=True, includes deleted datasets in
history dataset list
--visible TEXT Used when contents=True, includes only visible datasets in
history dataset list
--details TEXT Used when contents=True, includes dataset details. Set to
'all' for the most information
Thus with a simple query
$ parsec histories show_history 548c0777ac615645 --contents --deleted True | jq -S '.[0]'
We see the first deleted dataset in the history.
{
"create_time": "2017-05-02T16:18:54.272050",
"dataset_id": "93c926a0dabafde3",
"deleted": true,
"extension": "fasta",
"hid": 30,
"history_content_type": "dataset",
"history_id": "548c0777ac615645",
"id": "d643e34e1114cc52",
"name": "Feature Sequence Export Unique on data 27 and data 20",
"purged": false,
"state": "error",
"type": "file",
"type_id": "dataset-d643e34e1114cc52",
"update_time": "2017-05-02T16:47:57.807506",
"url": "/galaxy/api/histories/548c0777ac615645/contents/d643e34e1114cc52",
"visible": true
}
This gives us a dictionary containing the History’s metadata. With contents=False (the default), we only get a list of ids of the datasets contained within the History; with contents=True we would get metadata on each dataset. We can also directly access more detailed information on a particular dataset by passing its id to the show_dataset method:
$ parsec datasets_show_dataset 10a4b652da44e82a
{
"accessible": true,
"annotation": null,
"api_type": "file",
"create_time": "2015-02-27T23:46:27.642906",
"data_type": "galaxy.datatypes.data.Text",
"dataset_id": "10a4b652da44e82a",
"deleted": false,
"display_apps": [],
"display_types": [],
"download_url": "/api/histories/f3c2b0f3ecac9f02/contents/10a4b652da44e82a/display",
"extension": "fastq",
"file_ext": "fastq",
"file_path": null,
"file_size": 16527060,
"genome_build": "dm3",
"hda_ldda": "hda",
"hid": 1,
"history_content_type": "dataset",
"history_id": "f3c2b0f3ecac9f02",
"id": "10a4b652da44e82a",
"meta_files": [],
"metadata_data_lines": 4,
"metadata_dbkey": "dm3",
"misc_blurb": "15.8 MB",
"misc_info": "uploaded fastqsanger file",
"model_class": "HistoryDatasetAssociation",
"name": "C1_R2_1.chr4.fq",
"purged": false,
"resubmitted": false,
"state": "ok",
"tags": [],
"type": "file",
"update_time": "2015-02-27T23:46:34.659590",
"url": "/api/histories/f3c2b0f3ecac9f02/contents/10a4b652da44e82a",
"uuid": "ccad6f3a-f75d-472f-9142-2d4c39ad1a35",
"visible": true,
"visualizations": []
}
On JQ¶
It is worth it to look at some of the things possible with JQ for a moment. The above example may not be so exciting at first blush, but you can do incredible things with the combination of parsec, jq, and xargs. Here are some examples to consider:
find all histories with a public link, but not published in the shared-histories section, and print out their history name and the shared link.
$ parsec histories get_histories | \ jq '.[].id' | \ xargs -n 1 parsec histories show_history | \ jq '. | select(.published == false) | select(.importable == true) | [.published, .importable, .id, .username_and_slug] | @tsv' -r
reset the API keys for 30 users at once.
$ parsec users get_users | \ jq '.[] | \ select(.username | contains("janedoe")) | .id' | \ xargs -n 1 parsec users create_user_apikey
download all of the OK datasets in a set of histories
$ parsec histories get_histories | \ jq '.[].id' | \ # Or other, more complex filtering? xargs -n 1 parsec histories show_history | \ # Get history details jq '.state_ids.ok[]' | \ # Find OK datasets xargs -n 1 parsec datasets download_dataset --file_path '.' --use_default_filename # Download
View Workflows¶
Methods for accessing workflows are grouped under GalaxyInstance.workflows.*.
To get information on the Workflows currently in your account, use:
$ parsec workflows get_workflows
[
{
'id': 'e8b85ad72aefca86',
'name': u"TopHat + cufflinks part 1",
'url': '/api/workflows/e8b85ad72aefca86'
},
{
'id': 'b0631c44aa74526d',
'name': 'CuffDiff',
'url': '/api/workflows/b0631c44aa74526d'
}
]
For example, to further investigate a workflow, we can request:
$ parsec workflows show_workflow ded67e5aa1371841 | jq 'del(.steps)'
The workflow output is generally quite large as it embeds a full copy of the
workflow. In the above JQ command I have removed the steps attribute from
the output for brevity.
{
"annotation": "",
"model_class": "StoredWorkflow",
"latest_workflow_uuid": "94c40212-c4bb-43b7-a43b-eadc1a3b2894",
"id": "ded67e5aa1371841",
"url": "/galaxy/api/workflows/ded67e5aa1371841",
"deleted": false,
"tags": [],
"owner": "helena-rasche",
"name": "PAP 2017 Functional (v8.15)",
"inputs": {
"0": {
"value": "",
"uuid": "9397916e-afb7-4e48-b89e-d4c99bf202de",
"label": "Apollo Organism JSON File"
},
"2": {
"value": "",
"uuid": "eca835c6-328a-4698-a387-d0719b24d19d",
"label": "Genome Sequence"
},
"1": {
"value": "",
"uuid": "5511d038-e96b-49b2-998a-d037935f6e06",
"label": "Annotation Set"
}
},
"published": false
}
View Users¶
Methods for managing users are grouped under GalaxyInstance.users.*. User management is only available to Galaxy administrators, that is, the API key used to connect to Galaxy must be that of an admin account.
To get a list of users, call:
$ parsec users get_users
[
{
"username": "test",
"model_class": "User",
"email": "test@local.host",
"id": "f2db41e1fa331b3e"
},
...
]
In Depth Example¶
As a more detailed example, we’ll launch a simple workflow.
Step 1. What are the Inputs¶
$ parsec workflows show_workflow ded67e5aa1371841 | jq .inputs > inputs.json
In practice this file probably looks similar to this:
{
"0": {
"value": "",
"uuid": "9397916e-afb7-4e48-b89e-d4c99bf202de",
"label": "Apollo Organism JSON File"
},
"2": {
"value": "",
"uuid": "eca835c6-328a-4698-a387-d0719b24d19d",
"label": "Genome Sequence"
},
"1": {
"value": "",
"uuid": "5511d038-e96b-49b2-998a-d037935f6e06",
"label": "Annotation Set"
}
}
Step 2: Prepare History and Load Datasets¶
First, we’ll create a history to manage all of our work:
$ HISTORY_ID=$(parsec histories create_history | jq .id)
$ parsec histories update_history --name 'Parsec test'
Next we have to fetch some datasets. You could upload them:
$ parsec tools upload_file my-file.gff3 $HISTORY_ID
But in my case, I need to run a tool which produces them:
JOB_ID=$(parsec tools run_tool $HISTORY_ID edu.tamu.cpt2.webapollo.export \
'{"org_source|source_select": "direct", "org_source|org_raw": "Miro"}' | \
jq .id)
$ parsec jobs show_job .outputs $JOB_ID
By storing the job ID in a variable, we can make repeated requests to check on it. The second parsec statement fetches the output datasets from this step.
{
"fasta_out": {
"id": "61513e15ce98c986",
"src": "hda",
"uuid": "0de1442b-c410-4a38-b9ca-49cff973d9b8"
},
"gff_out": {
"id": "62ee69adcf74378c",
"src": "hda",
"uuid": "887aaf6f-ed07-4ee8-a396-c16612f83d83"
},
"json_out": {
"id": "1f73e96543934ac8",
"src": "hda",
"uuid": "3be3d364-83c5-4a23-87fa-ebd8c27f2094"
}
}
Step 3: Invoking the Workflow¶
Remembering back to the inputs in step 1, we will match them up and create an inputs.json file
- 0 / organism json file => json_out
- 1 / genome sequence => gff_out
- 2 / annotation set => fasta_out
This gives us an inputs.json that looks like so:
{
"0": {
"id": "1f73e96543934ac8",
"src": "hda"
},
"1": {
"id": "62ee69adcf74378c",
"src": "hda"
},
"2": {
"id": "61513e15ce98c986",
"src": "hda"
}
}
We can now invoke our workflow using parsec! Since the inputs is a JSON parameter, it can be supplied many different ways for your convenience. All of the following behave identically.
$ cat params.json | parsec jobs search_jobs -; # Stdin
$ parsec jobs search_jobs params.json; # Filename
$ parsec jobs search_jobs $(cat params.json); # String argument
Running the invocation:
$ parsec workflows invoke_workflow ded67e5aa1371841 --inputs inputs.json --history_id $HISTORY_ID
Produces a very succinct workflow launch output:
{
"uuid": "94246003-2f8b-11e7-9427-20474784cc00",
"state": "new",
"workflow_id": "3daf5606d767a471",
"id": "c7f60cfda02f0f46",
"update_time": "2017-05-02T23:03:39.693288",
"model_class": "WorkflowInvocation",
"history_id": "0d17c6f8cd8d49a5"
}
We can now use parsec to check on the status of all of the datasets:
$ parsec workflows show_invocation 3daf5606d767a471 c7f60cfda02f0f46 | jq '.steps[].state' | sort | uniq -c
3 "running"
72 "new"
3 null
1 "ok"
Or we can use one of the utility scripts to wait on that workflow to finish before continuing on to some other task:
$ parsec utils wait_on_invocation 3daf5606d767a471 c7f60cfda02f0f46 && ...
License¶
Copyright 2016-2017 Galaxy IUC
Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Support¶
This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)
Cookbook¶
This page will contain more easy “recipes” for using parsec as time goes on. Short tips and tricks that can help you use it more effectively, or short recipes that can document how to do more complex tasks.
Talking to multiple Galaxies¶
If you are regularly switching between multiple Galaxy instances, you’ll probably want to take advantage of the environment variable for specifying a Galaxy instance. E.g.:
$ PARSEC_GALAXY_INSTANCE=uni-admin parsec config get_config | jq .brand
"Internal"
$ PARSEC_GALAXY_INSTANCE=uni-public parsec config get_config | jq .brand
"Public"
You could easily set these at the top of a parsec script you’ve built and all commands from there on would talk to the same Galaxy instance.
Capturing execution state as XUnit Output¶
If you find yourself building a pipeline with parsec and jq, you might find
yourself wanting to produce the output in a machine-legible format such as
XUnit. parsec now ships with a (very alpha) script to help with this.
parsec utils xunit_xargs provides an xargs-like experience, except it
produces XUnit formatted output. We’ll run through a quick example of this:
parsec histories get_histories | \
jq '.[].id' -r | \
head -n 3 | \
parsec utils xunit_xargs parsec histories get_status \| jq .percent_complete \| parsec utils cmp eq 100
This command will fetch the first three histories, and then attempt to run
parsec histories get_status <history_id> | jq .percent_complete for each
history id passed in.
<?xml version="1.0" ?>
<testsuites errors="0" failures="1" tests="3" time="1.6388022899627686">
<testsuite errors="0" failures="1" name="Parsec XX" skipped="0" tests="3" time="1.6388022899627686">
<testcase classname="parsec.histories.get_status.769f01a3981796db_|.jq..percent_complete.|.parsec.utils.cmp.eq.100" name="parsec.histories.get_status.769f01a3981796db_" time="0.537762"/>
<testcase classname="parsec.histories.get_status.83fbc32772cb5fcf_|.jq..percent_complete.|.parsec.utils.cmp.eq.100" name="parsec.histories.get_status.83fbc32772cb5fcf_" time="0.534841"/>
<testcase classname="parsec.histories.get_status.90c9282cb8718062_|.jq..percent_complete.|.parsec.utils.cmp.eq.100" name="parsec.histories.get_status.90c9282cb8718062_" time="0.566199">
<failure message="Command 'parsec histories get_status 90c9282cb8718062 | jq .percent_complete | parsec utils cmp eq 100' returned non-zero exit status 1" type="failure">Traceback (most recent call last):
File "xunit_xargs.py", line 95, in cli
output = check_output(' '.join(built_command), shell=True, stderr=stderr)
File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
**kwargs).stdout
File "/usr/lib/python3.5/subprocess.py", line 708, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'parsec histories get_status 90c9282cb8718062 | jq .percent_complete | parsec utils cmp eq 100' returned non-zero exit status 1
</failure>
<system-err>97.82608695652173 != 100.0</system-err>
</testcase>
</testsuite>
</testsuites>
Here we can see the example output, every history ID that went in came out as a test case. One of them didn’t pass a test we cared about and was marked as a failure.
Commands¶
parsec is a set of wrappers for BioBlend’s API. It builds a set of small,
useful utilities for talking to Galaxy servers. Each utility is implemented as
a subcommand of parsec. This section of the documentation
describes these commands.
config¶
This section is auto-generated from the help text for the parsec command
config.
get_config command¶
Usage:
parsec config get_config [OPTIONS]
Help
Get a list of attributes about the Galaxy instance. More attributes will be present if the user is an admin.
Output
- A list of attributes.
For example:
{u'allow_library_path_paste': False, u'allow_user_creation': True, u'allow_user_dataset_purge': True, u'allow_user_deletion': False, u'enable_unique_workflow_defaults': False, u'ftp_upload_dir': u'/SOMEWHERE/galaxy/ftp_dir', u'ftp_upload_site': u'galaxy.com', u'library_import_dir': u'None', u'logo_url': None, u'support_url': u'https://galaxyproject.org/support', u'terms_url': None, u'user_library_import_dir': None, u'wiki_url': u'https://galaxyproject.org/'}
Options:
-h, --help Show this message and exit.
get_version command¶
Usage:
parsec config get_version [OPTIONS]
Help
Get the current version of the Galaxy instance. This functionality is available since Galaxy release_15.03.
Output
Version of the Galaxy instanceFor example:
{'extra': {}, 'version_major': '17.01'}
Options:
-h, --help Show this message and exit.
datasets¶
This section is auto-generated from the help text for the parsec command
datasets.
download_dataset command¶
Usage:
parsec datasets download_dataset [OPTIONS] DATASET_ID
Help
Download a dataset to file or in memory. If the dataset state is not ‘ok’, a DatasetStateException will be thrown.
Output
- If a file_path argument is not provided, returns a dict containing the file_content.
- Otherwise returns nothing.
Options:
--file_path TEXT If this argument is provided, the dataset will be
streamed to disk at that path (should be a directory
if use_default_filename=True). If the file_path
argument is not provided, the dataset content is
loaded into memory and returned by the method (Memory
consumption may be heavy as the entire file will be in
memory).
--use_default_filename If this argument is True, the exported file will be
saved as file_path/%s, where %s is the dataset name.
If this argument is False, file_path is assumed to
contain the full file path including the filename.
[default: True]
--wait_for_completion This parameter is deprecated and ignored, it will be
removed in BioBlend 0.12. [default: True]
--maxwait FLOAT Total time (in seconds) to wait for the dataset state
to become terminal. If the dataset state is not
terminal within this time, a
``DatasetTimeoutException`` will be thrown. [default:
12000]
-h, --help Show this message and exit.
show_dataset command¶
Usage:
parsec datasets show_dataset [OPTIONS] DATASET_ID
Help
Get details about a given dataset. This can be a history or a library dataset.
Output
Options:
--deleted Whether to return results for a deleted dataset
--hda_ldda TEXT Whether to show a history dataset ('hda' - the default) or
library dataset ('ldda'). [default: hda]
-h, --help Show this message and exit.
datatypes¶
This section is auto-generated from the help text for the parsec command
datatypes.
get_datatypes command¶
Usage:
parsec datatypes get_datatypes [OPTIONS]
Help
Get the list of all installed datatypes.
Output
- A list of datatype names.
For example:
[u'snpmatrix', u'snptest', u'tabular', u'taxonomy', u'twobit', u'txt', u'vcf', u'wig', u'xgmml', u'xml']
Options:
--extension_only TEXT
--upload_only TEXT
-h, --help Show this message and exit.
get_sniffers command¶
Usage:
parsec datatypes get_sniffers [OPTIONS]
Help
Get the list of all installed sniffers.
Output
- A list of sniffer names.
For example:
[u'galaxy.datatypes.tabular:Vcf', u'galaxy.datatypes.binary:TwoBit', u'galaxy.datatypes.binary:Bam', u'galaxy.datatypes.binary:Sff', u'galaxy.datatypes.xml:Phyloxml', u'galaxy.datatypes.xml:GenericXml', u'galaxy.datatypes.sequence:Maf', u'galaxy.datatypes.sequence:Lav', u'galaxy.datatypes.sequence:csFasta']
Options:
-h, --help Show this message and exit.
folders¶
This section is auto-generated from the help text for the parsec command
folders.
create_folder command¶
Usage:
parsec folders create_folder [OPTIONS] PARENT_FOLDER_ID NAME
Help
Create a folder.
Output
details of the updated folder
Options:
--description TEXT folder's description
-h, --help Show this message and exit.
delete_folder command¶
Usage:
parsec folders delete_folder [OPTIONS] FOLDER_ID
Help
Marks the folder with the given id as deleted (or removes the deleted mark if the undelete param is True).
Output
Options:
--undelete If set to True, the folder will be undeleted (i.e. the `deleted`
mark will be removed)
-h, --help Show this message and exit.
get_permissions command¶
Usage:
parsec folders get_permissions [OPTIONS] FOLDER_ID SCOPE
Help
Get the permissions of a folder.
Output
dictionary including details of the folder
Options:
-h, --help Show this message and exit.
set_permissions command¶
Usage:
parsec folders set_permissions [OPTIONS] FOLDER_ID
Help
Set the permissions of a folder.
Output
dictionary including details of the folder
Options:
--action TEXT action to execute, only "set_permissions" is supported.
[default: set_permissions]
--add_ids TEXT list of role IDs which can add datasets to the folder
--manage_ids TEXT list of role IDs which can manage datasets in the folder
--modify_ids TEXT list of role IDs which can modify datasets in the folder
-h, --help Show this message and exit.
show_folder command¶
Usage:
parsec folders show_folder [OPTIONS] FOLDER_ID
Help
Display information about a folder.
Output
dictionary including details of the folder
Options:
--contents True to get the contents of the folder, rather than just the
folder details.
-h, --help Show this message and exit.
update_folder command¶
Usage:
parsec folders update_folder [OPTIONS] FOLDER_ID NAME
Help
Update folder information.
Output
details of the updated folder
Options:
--description TEXT folder's description
-h, --help Show this message and exit.
forms¶
This section is auto-generated from the help text for the parsec command
forms.
create_form command¶
Usage:
parsec forms create_form [OPTIONS] FORM_XML_TEXT
Help
Create a new form.
Output
Options:
-h, --help Show this message and exit.
get_forms command¶
Usage:
parsec forms get_forms [OPTIONS]
Help
Get the list of all forms.
Output
Options:
-h, --help Show this message and exit.
show_form command¶
Usage:
parsec forms show_form [OPTIONS] FORM_ID
Help
Get details of a given form.
Output
- A description of the given form.
For example:
{u'desc': u'here it is ', u'fields': [], u'form_definition_current_id': u'f2db41e1fa331b3e', u'id': u'f2db41e1fa331b3e', u'layout': [], u'model_class': u'FormDefinition', u'name': u'First form', u'url': u'/api/forms/f2db41e1fa331b3e'}
Options:
-h, --help Show this message and exit.
ftpfiles¶
This section is auto-generated from the help text for the parsec command
ftpfiles.
get_ftp_files command¶
Usage:
parsec ftpfiles get_ftp_files [OPTIONS]
Help
Get a list of local files.
Output
A list of dicts with details on individual files on FTP
Options:
--deleted TEXT
-h, --help Show this message and exit.
genomes¶
This section is auto-generated from the help text for the parsec command
genomes.
get_genomes command¶
Usage:
parsec genomes get_genomes [OPTIONS]
Help
Returns a list of installed genomes
Output
Options:
-h, --help Show this message and exit.
install_genome command¶
Usage:
parsec genomes install_genome [OPTIONS]
Help
Download and/or index a genome.
Output
- dict( status: ‘ok’, job: <job ID> )
- If error: dict( status: ‘error’, error: <error message> )
Options:
--func TEXT Allowed values: 'download', Download and index; 'index',
Index only [default: download]
--source TEXT Data source for this build. Can be: UCSC, Ensembl, NCBI,
URL
--dbkey TEXT DB key of the build to download, ignored unless 'UCSC'
is specified as the source
--ncbi_name TEXT NCBI's genome identifier, ignored unless NCBI is
specified as the source
--ensembl_dbkey TEXT Ensembl's genome identifier, ignored unless Ensembl is
specified as the source
--url_dbkey TEXT DB key to use for this build, ignored unless URL is
specified as the source
--indexers TEXT POST array of indexers to run after downloading
(indexers[] = first, indexers[] = second, ...)
-h, --help Show this message and exit.
show_genome command¶
Usage:
parsec genomes show_genome [OPTIONS] ID
Help
Returns information about build <id>
Output
Options:
--num TEXT num
--chrom TEXT chrom
--low TEXT low
--high TEXT high
-h, --help Show this message and exit.
groups¶
This section is auto-generated from the help text for the parsec command
groups.
add_group_role command¶
Usage:
parsec groups add_group_role [OPTIONS] GROUP_ID ROLE_ID
Help
Add a role to the given group.
Output
Added group role’s info
Options:
-h, --help Show this message and exit.
add_group_user command¶
Usage:
parsec groups add_group_user [OPTIONS] GROUP_ID USER_ID
Help
Add a user to the given group.
Output
Added group user’s info
Options:
-h, --help Show this message and exit.
create_group command¶
Usage:
parsec groups create_group [OPTIONS] GROUP_NAME
Help
Create a new group.
Output
- A (size 1) list with newly created group
details, like:
[{u'id': u'7c9636938c3e83bf', u'model_class': u'Group', u'name': u'My Group Name', u'url': u'/api/groups/7c9636938c3e83bf'}]
Options:
--user_ids TEXT A list of encoded user IDs to add to the new group
--role_ids TEXT A list of encoded role IDs to add to the new group
-h, --help Show this message and exit.
delete_group_role command¶
Usage:
parsec groups delete_group_role [OPTIONS] GROUP_ID ROLE_ID
Help
Remove a role from the given group.
Output
Options:
-h, --help Show this message and exit.
delete_group_user command¶
Usage:
parsec groups delete_group_user [OPTIONS] GROUP_ID USER_ID
Help
Remove a user from the given group.
Output
Options:
-h, --help Show this message and exit.
get_group_roles command¶
Usage:
parsec groups get_group_roles [OPTIONS] GROUP_ID
Help
Get the list of roles associated to the given group.
Output
List of group roles’ info
Options:
-h, --help Show this message and exit.
get_group_users command¶
Usage:
parsec groups get_group_users [OPTIONS] GROUP_ID
Help
Get the list of users associated to the given group.
Output
List of group users’ info
Options:
-h, --help Show this message and exit.
get_groups command¶
Usage:
parsec groups get_groups [OPTIONS]
Help
Get all (not deleted) groups.
Output
- A list of dicts with details on individual groups.
For example:
[{'id': '33abac023ff186c2', 'model_class': 'Group', 'name': 'Listeria', 'url': '/api/groups/33abac023ff186c2'}, {'id': '73187219cd372cf8', 'model_class': 'Group', 'name': 'LPN', 'url': '/api/groups/73187219cd372cf8'}]
Options:
-h, --help Show this message and exit.
show_group command¶
Usage:
parsec groups show_group [OPTIONS] GROUP_ID
Help
Get details of a given group.
Output
- A description of group
For example:
{'id': '33abac023ff186c2', 'model_class': 'Group', 'name': 'Listeria', 'roles_url': '/api/groups/33abac023ff186c2/roles', 'url': '/api/groups/33abac023ff186c2', 'users_url': '/api/groups/33abac023ff186c2/users'}
Options:
-h, --help Show this message and exit.
update_group command¶
Usage:
parsec groups update_group [OPTIONS] GROUP_ID
Help
Update a group.
Output
Options:
--group_name TEXT A new name for the group. If None, the group name is not
changed.
--user_ids TEXT New list of encoded user IDs for the group. It will
substitute the previous list of users (with [] if not
specified)
--role_ids TEXT New list of encoded role IDs for the group. It will
substitute the previous list of roles (with [] if not
specified)
-h, --help Show this message and exit.
histories¶
This section is auto-generated from the help text for the parsec command
histories.
create_dataset_collection command¶
Usage:
parsec histories create_dataset_collection [OPTIONS] HISTORY_ID
Help
Create a new dataset collection
Output
Options:
-h, --help Show this message and exit.
create_history command¶
Usage:
parsec histories create_history [OPTIONS]
Help
Create a new history, optionally setting the name.
Output
Dictionary containing information about newly created history
Options:
--name TEXT Optional name for new history
-h, --help Show this message and exit.
create_history_tag command¶
Usage:
parsec histories create_history_tag [OPTIONS] HISTORY_ID TAG
Help
Create history tag
Output
- A dictionary with information regarding the tag.
For example:
{'id': 'f792763bee8d277a', 'model_class': 'HistoryTagAssociation', 'user_tname': 'NGS_PE_RUN', 'user_value': None}
Options:
-h, --help Show this message and exit.
delete_dataset command¶
Usage:
parsec histories delete_dataset [OPTIONS] HISTORY_ID DATASET_ID
Help
Mark corresponding dataset as deleted.
Output
Options:
--purge if ``True``, also purge (permanently delete) the dataset
-h, --help Show this message and exit.
delete_dataset_collection command¶
Usage:
parsec histories delete_dataset_collection [OPTIONS] HISTORY_ID
Help
Mark corresponding dataset collection as deleted.
Output
Options:
-h, --help Show this message and exit.
delete_history command¶
Usage:
parsec histories delete_history [OPTIONS] HISTORY_ID
Help
Delete a history.
Output
Options:
--purge if ``True``, also purge (permanently delete) the history
-h, --help Show this message and exit.
download_dataset command¶
Usage:
parsec histories download_dataset [OPTIONS] HISTORY_ID DATASET_ID
Help
Deprecated since version 0.8.0: Use download_dataset() instead.
Output
Options:
--use_default_filename TEXT [default: True]
-h, --help Show this message and exit.
download_history command¶
Usage:
parsec histories download_history [OPTIONS] HISTORY_ID JEHA_ID OUTF
Help
Download a history export archive. Use export_history() to create an export.
Output
Options:
--chunk_size INTEGER how many bytes at a time should be read into memory
[default: 4096]
-h, --help Show this message and exit.
export_history command¶
Usage:
parsec histories export_history [OPTIONS] HISTORY_ID
Help
Start a job to create an export archive for the given history.
Output
jeha_idof the export, or empty ifwaitisFalse- and the export is not ready.
Options:
--gzip create .tar.gz archive if ``True``, else .tar [default:
True]
--include_hidden whether to include hidden datasets in the export
--include_deleted whether to include deleted datasets in the export
--wait if ``True``, block until the export is ready; else, return
immediately
-h, --help Show this message and exit.
get_current_history command¶
Usage:
parsec histories get_current_history [OPTIONS]
Help
Deprecated since version 0.5.2: Use get_most_recently_used_history() instead.
Output
Options:
-h, --help Show this message and exit.
get_histories command¶
Usage:
parsec histories get_histories [OPTIONS]
Help
Get all histories or filter the specific one(s) via the provided name or history_id. Provide only one argument, name or history_id, but not both.
Output
- Return a list of history element dicts. If more than one
- history matches the given
name, return the list of all the histories with the given name
Options:
--history_id TEXT Encoded history ID to filter on
--name TEXT Name of history to filter on
--deleted TEXT
-h, --help Show this message and exit.
get_most_recently_used_history command¶
Usage:
parsec histories get_most_recently_used_history [OPTIONS]
Help
Returns the current user’s most recently used history (not deleted).
Output
Options:
-h, --help Show this message and exit.
get_status command¶
Usage:
parsec histories get_status [OPTIONS] HISTORY_ID
Help
Returns the state of this history
Output
- A dict documenting the current state of the history. Has the following keys:
- ‘state’ = This is the current state of the history, such as ok, error, new etc. ‘state_details’ = Contains individual statistics for various dataset states. ‘percent_complete’ = The overall number of datasets processed to completion.
Options:
-h, --help Show this message and exit.
show_dataset command¶
Usage:
parsec histories show_dataset [OPTIONS] HISTORY_ID DATASET_ID
Help
Get details about a given history dataset.
Output
Options:
-h, --help Show this message and exit.
show_dataset_collection command¶
Usage:
parsec histories show_dataset_collection [OPTIONS] HISTORY_ID
Help
Get details about a given history dataset collection.
Output
Options:
-h, --help Show this message and exit.
show_dataset_provenance command¶
Usage:
parsec histories show_dataset_provenance [OPTIONS] HISTORY_ID DATASET_ID
Help
Get details related to how dataset was created (id, job_id, tool_id, stdout, stderr, parameters, inputs, etc…).
Output
Options:
--follow If ``follow`` is ``True``, recursively fetch dataset provenance
information for all inputs and their inputs, etc...
-h, --help Show this message and exit.
show_history command¶
Usage:
parsec histories show_history [OPTIONS] HISTORY_ID
Help
Get details of a given history. By default, just get the history meta information.
Output
details of the given history
Options:
--contents When ``True``, the complete list of datasets in the given
history.
--deleted TEXT Used when contents=True, includes deleted datasets in history
dataset list
--visible TEXT Used when contents=True, includes only visible datasets in
history dataset list
--details TEXT Used when contents=True, includes dataset details. Set to
'all' for the most information
--types TEXT ???
-h, --help Show this message and exit.
show_matching_datasets command¶
Usage:
parsec histories show_matching_datasets [OPTIONS] HISTORY_ID
Help
Get dataset details for matching datasets within a history.
Output
Options:
--name_filter TEXT Only datasets whose name matches the ``name_filter``
regular expression will be returned; use plain strings for
exact matches and None to match all datasets in the
history
-h, --help Show this message and exit.
undelete_history command¶
Usage:
parsec histories undelete_history [OPTIONS] HISTORY_ID
Help
Undelete a history
Output
Options:
-h, --help Show this message and exit.
update_dataset command¶
Usage:
parsec histories update_dataset [OPTIONS] HISTORY_ID DATASET_ID
Help
Update history dataset metadata. Some of the attributes that can be modified are documented below.
Output
- details of the updated dataset (for Galaxy release_15.01 and
- earlier only the updated attributes)
Warning
The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).
Options:
--annotation TEXT Replace history dataset annotation with given string
--deleted Mark or unmark history dataset as deleted
--genome_build TEXT Replace history dataset genome build (dbkey)
--name TEXT Replace history dataset name with the given string
--visible Mark or unmark history dataset as visible
-h, --help Show this message and exit.
update_dataset_collection command¶
Usage:
parsec histories update_dataset_collection [OPTIONS] HISTORY_ID
Help
Update history dataset collection metadata. Some of the attributes that can be modified are documented below.
Output
the updated dataset collection attributesWarning
The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).
Options:
--deleted Mark or unmark history dataset collection as deleted
--name TEXT Replace history dataset collection name with the given string
--visible Mark or unmark history dataset collection as visible
-h, --help Show this message and exit.
update_history command¶
Usage:
parsec histories update_history [OPTIONS] HISTORY_ID
Help
Update history metadata information. Some of the attributes that can be modified are documented below.
Output
- details of the updated history (for Galaxy release_15.01 and
- earlier only the updated attributes)
Warning
The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).
Options:
--annotation TEXT Replace history annotation with given string
--deleted Mark or unmark history as deleted
--importable Mark or unmark history as importable
--name TEXT Replace history name with the given string
--published Mark or unmark history as published
--purged If True, mark history as purged (permanently deleted).
Ignored on Galaxy release_15.01 and earlier
--tags TEXT Replace history tags with the given list
-h, --help Show this message and exit.
upload_dataset_from_library command¶
Usage:
parsec histories upload_dataset_from_library [OPTIONS] HISTORY_ID
Help
Upload a dataset into the history from a library. Requires the library dataset ID, which can be obtained from the library contents.
Output
Options:
-h, --help Show this message and exit.
jobs¶
This section is auto-generated from the help text for the parsec command
jobs.
get_jobs command¶
Usage:
parsec jobs get_jobs [OPTIONS]
Help
Get the list of jobs of the current user.
Output
Options:
-h, --help Show this message and exit.
get_state command¶
Usage:
parsec jobs get_state [OPTIONS] JOB_ID
Help
Display the current state for a given job of the current user.
Output
- state of the given job among the following values: new,
- queued, running, waiting, ok. If the state cannot be retrieved, an empty string is returned.
New in version 0.5.3.
Options:
-h, --help Show this message and exit.
search_jobs command¶
Usage:
parsec jobs search_jobs [OPTIONS] JOB_INFO
Help
Return jobs for the current user based payload content.
Output
Options:
-h, --help Show this message and exit.
show_job command¶
Usage:
parsec jobs show_job [OPTIONS] JOB_ID
Help
Get details of a given job of the current user.
Output
- A description of the given job.
For example:
{u'create_time': u'2014-03-01T16:17:29.828624', u'exit_code': 0, u'id': u'a799d38679e985db', u'inputs': {u'input': {u'id': u'ebfb8f50c6abde6d', u'src': u'hda'}}, u'model_class': u'Job', u'outputs': {u'output': {u'id': u'a799d38679e985db', u'src': u'hda'}}, u'params': {u'chromInfo': u'"/opt/galaxy-central/tool-data/shared/ucsc/chrom/?.len"', u'dbkey': u'"?"', u'seq_col': u'"2"', u'title_col': u'["1"]'}, u'state': u'ok', u'tool_id': u'tab2fasta', u'update_time': u'2014-03-01T16:17:31.930728'}
Options:
--full_details when ``True``, the complete list of details for the given job.
-h, --help Show this message and exit.
libraries¶
This section is auto-generated from the help text for the parsec command
libraries.
copy_from_dataset command¶
Usage:
parsec libraries copy_from_dataset [OPTIONS] LIBRARY_ID DATASET_ID
Help
Copy a Galaxy dataset into a library.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded files. If not
provided, the root folder will be used
--message TEXT message for copying action
-h, --help Show this message and exit.
create_folder command¶
Usage:
parsec libraries create_folder [OPTIONS] LIBRARY_ID FOLDER_NAME
Help
Create a folder in a library.
Output
Options:
--description TEXT description of the new folder in the data library
--base_folder_id TEXT id of the folder where to create the new folder. If not
provided, the root folder will be used
-h, --help Show this message and exit.
create_library command¶
Usage:
parsec libraries create_library [OPTIONS] NAME
Help
Create a data library with the properties defined in the arguments.
Output
- Details of the created library.
For example:
{'id': 'f740ab636b360a70', 'name': 'Library from bioblend', 'url': '/api/libraries/f740ab636b360a70'}
Options:
--description TEXT Optional data library description
--synopsis TEXT Optional data library synopsis
-h, --help Show this message and exit.
delete_library command¶
Usage:
parsec libraries delete_library [OPTIONS] LIBRARY_ID
Help
Delete a data library.
Output
Options:
-h, --help Show this message and exit.
delete_library_dataset command¶
Usage:
parsec libraries delete_library_dataset [OPTIONS] LIBRARY_ID DATASET_ID
Help
Delete a library dataset in a data library.
Output
- A dictionary containing the dataset id and whether the dataset
has been deleted. For example:
{u'deleted': True, u'id': u'60e680a037f41974'}
Options:
--purged Indicate that the dataset should be purged (permanently deleted)
-h, --help Show this message and exit.
get_folders command¶
Usage:
parsec libraries get_folders [OPTIONS] LIBRARY_ID
Help
Get all the folders or filter specific one(s) via the provided name or folder_id in data library with id library_id. Provide only one argument: name or folder_id, but not both.
Output
list of dicts each containing basic information about a folder
Options:
--folder_id TEXT filter for folder by folder id
--name TEXT filter for folder by name. For ``name`` specify the full
path of the folder starting from the library's root folder,
e.g. ``/subfolder/subsubfolder``.
-h, --help Show this message and exit.
get_libraries command¶
Usage:
parsec libraries get_libraries [OPTIONS]
Help
Get all the libraries or filter for specific one(s) via the provided name or ID. Provide only one argument: name or library_id, but not both.
Output
list of dicts each containing basic information about a library
Options:
--library_id TEXT filter for library by library id
--name TEXT If ``name`` is set and multiple names match the given name,
all the libraries matching the argument will be returned
--deleted If set to ``True``, return libraries that have been deleted
-h, --help Show this message and exit.
get_library_permissions command¶
Usage:
parsec libraries get_library_permissions [OPTIONS] LIBRARY_ID
Help
Get the permessions for a library.
Output
dictionary with all applicable permissions’ values
Options:
-h, --help Show this message and exit.
set_library_permissions command¶
Usage:
parsec libraries set_library_permissions [OPTIONS] LIBRARY_ID
Help
Set the permissions for a library. Note: it will override all security for this library even if you leave out a permission type.
Output
Options:
--access_in TEXT list of role ids
--modify_in TEXT list of role ids
--add_in TEXT list of role ids
--manage_in TEXT list of role ids
-h, --help Show this message and exit.
show_dataset command¶
Usage:
parsec libraries show_dataset [OPTIONS] LIBRARY_ID DATASET_ID
Help
Get details about a given library dataset. The required library_id can be obtained from the datasets’s library content details.
Output
- A dictionary containing information about the dataset in the
- library
Options:
-h, --help Show this message and exit.
show_folder command¶
Usage:
parsec libraries show_folder [OPTIONS] LIBRARY_ID FOLDER_ID
Help
Get details about a given folder. The required folder_id can be obtained from the folder’s library content details.
Output
Options:
-h, --help Show this message and exit.
show_library command¶
Usage:
parsec libraries show_library [OPTIONS] LIBRARY_ID
Help
Get information about a library.
Output
details of the given library
Options:
--contents True if want to get contents of the library (rather than just the
library details)
-h, --help Show this message and exit.
upload_file_contents command¶
Usage:
parsec libraries upload_file_contents [OPTIONS] LIBRARY_ID PASTED_CONTENT
Help
Upload pasted_content to a data library as a new file.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded file. If not
provided, the root folder will be used
--file_type TEXT Galaxy file format name [default: auto]
--dbkey TEXT Dbkey [default: ?]
-h, --help Show this message and exit.
upload_file_from_local_path command¶
Usage:
parsec libraries upload_file_from_local_path [OPTIONS] LIBRARY_ID
Help
Read local file contents from file_local_path and upload data to a library.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded file. If not
provided, the root folder will be used
--file_type TEXT Galaxy file format name [default: auto]
--dbkey TEXT Dbkey [default: ?]
-h, --help Show this message and exit.
upload_file_from_server command¶
Usage:
parsec libraries upload_file_from_server [OPTIONS] LIBRARY_ID SERVER_DIR
Help
Upload all files in the specified subdirectory of the Galaxy library import directory to a library.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded files. If
not provided, the root folder will be used
--file_type TEXT Galaxy file format name [default: auto]
--dbkey TEXT Dbkey [default: ?]
--link_data_only TEXT either 'copy_files' (default) or 'link_to_files'.
Setting to 'link_to_files' symlinks instead of copying
the files
--roles TEXT ???
-h, --help Show this message and exit.
upload_file_from_url command¶
Usage:
parsec libraries upload_file_from_url [OPTIONS] LIBRARY_ID FILE_URL
Help
Upload a file to a library from a URL.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded file. If not
provided, the root folder will be used
--file_type TEXT Galaxy file format name [default: auto]
--dbkey TEXT Dbkey [default: ?]
-h, --help Show this message and exit.
upload_from_galaxy_filesystem command¶
Usage:
parsec libraries upload_from_galaxy_filesystem [OPTIONS] LIBRARY_ID
Help
Upload a set of files already present on the filesystem of the Galaxy server to a library.
Output
Options:
--folder_id TEXT id of the folder where to place the uploaded files. If
not provided, the root folder will be used
--file_type TEXT Galaxy file format name [default: auto]
--dbkey TEXT Dbkey [default: ?]
--link_data_only TEXT either 'copy_files' (default) or 'link_to_files'.
Setting to 'link_to_files' symlinks instead of copying
the files
--roles TEXT ???
-h, --help Show this message and exit.
wait_for_dataset command¶
Usage:
parsec libraries wait_for_dataset [OPTIONS] LIBRARY_ID DATASET_ID
Help
Wait until the library dataset state is terminal (‘ok’, ‘empty’, ‘error’, ‘discarded’ or ‘failed_metadata’).
Output
- A dictionary containing information about the dataset in the
- library
Options:
--maxwait FLOAT Total time (in seconds) to wait for the dataset state to
become terminal. If the dataset state is not terminal within
this time, a ``DatasetTimeoutException`` will be thrown.
[default: 12000]
--interval FLOAT Time (in seconds) to wait between 2 consecutive checks.
[default: 3]
-h, --help Show this message and exit.
quotas¶
This section is auto-generated from the help text for the parsec command
quotas.
create_quota command¶
Usage:
parsec quotas create_quota [OPTIONS] NAME DESCRIPTION AMOUNT OPERATION
Help
Create a new quota
Output
- A description of quota.
For example:
{u'url': '/galaxy/api/quotas/386f14984287a0f7', u'model_class': 'Quota', u'message': "Quota 'Testing' has been created with 1 associated users and 0 associated groups.", u'id': '386f14984287a0f7', u'name': 'Testing'}
Options:
--default TEXT Whether or not this is a default quota. Valid values are
``no``, ``unregistered``, ``registered``. None is equivalent
to ``no``. [default: no]
--in_users TEXT A list of user IDs or user emails.
--in_groups TEXT A list of group IDs or names.
-h, --help Show this message and exit.
delete_quota command¶
Usage:
parsec quotas delete_quota [OPTIONS] QUOTA_ID
Help
Delete a quota
Output
- A description of the changes, mentioning the deleted quota.
For example:
"Deleted 1 quotas: Testing-B"
Options:
-h, --help Show this message and exit.
get_quotas command¶
Usage:
parsec quotas get_quotas [OPTIONS]
Help
Get a list of quotas
Output
- A list of dicts with details on individual quotas.
For example:
[{u'id': u'0604c8a56abe9a50', u'model_class': u'Quota', u'name': u'test ', u'url': u'/api/quotas/0604c8a56abe9a50'}, {u'id': u'1ee267091d0190af', u'model_class': u'Quota', u'name': u'workshop', u'url': u'/api/quotas/1ee267091d0190af'}]
Options:
--deleted Only return quota(s) that have been deleted
-h, --help Show this message and exit.
show_quota command¶
Usage:
parsec quotas show_quota [OPTIONS] QUOTA_ID
Help
Display information on a quota
Output
- A description of quota.
For example:
{u'bytes': 107374182400, u'default': [], u'description': u'just testing', u'display_amount': u'100.0 GB', u'groups': [], u'id': u'0604c8a56abe9a50', u'model_class': u'Quota', u'name': u'test ', u'operation': u'=', u'users': []}
Options:
--deleted Search for quota in list of ones already marked as deleted
-h, --help Show this message and exit.
undelete_quota command¶
Usage:
parsec quotas undelete_quota [OPTIONS] QUOTA_ID
Help
Undelete a quota
Output
- A description of the changes, mentioning the undeleted quota.
For example:
"Undeleted 1 quotas: Testing-B"
Options:
-h, --help Show this message and exit.
update_quota command¶
Usage:
parsec quotas update_quota [OPTIONS] QUOTA_ID
Help
Update an existing quota
Output
- A semicolon separated list of changes to the quota.
For example:
"Quota 'Testing-A' has been renamed to 'Testing-B'; Quota 'Testing-e' is now '-100.0 GB'; Quota 'Testing-B' is now the default for unregistered users"
Options:
--name TEXT Name for the new quota. This must be unique within a
Galaxy instance.
--description TEXT Quota description. If you supply this parameter, but not
the name, an error will be thrown.
--amount TEXT Quota size (E.g. ``10000MB``, ``99 gb``, ``0.2T``,
``unlimited``)
--operation TEXT One of (``+``, ``-``, ``=``). If you wish to change this
value, you must also provide the ``amount``, otherwise it
will not take effect.
--default TEXT Whether or not this is a default quota. Valid values are
``no``, ``unregistered``, ``registered``. Calling this
method with ``default="no"`` on a non-default quota will
throw an error. Not passing this parameter is equivalent
to passing ``no``. [default: no]
--in_users TEXT A list of user IDs or user emails.
--in_groups TEXT A list of group IDs or names.
-h, --help Show this message and exit.
roles¶
This section is auto-generated from the help text for the parsec command
roles.
create_role command¶
Usage:
parsec roles create_role [OPTIONS] ROLE_NAME DESCRIPTION
Help
Create a new role.
Output
- A (size 1) list with newly created role
details, like:
[{u'description': u'desc', u'url': u'/api/roles/ebfb8f50c6abde6d', u'model_class': u'Role', u'type': u'admin', u'id': u'ebfb8f50c6abde6d', u'name': u'Foo'}]
Options:
--user_ids TEXT A list of encoded user IDs to add to the new role
--group_ids TEXT A list of encoded group IDs to add to the new role
-h, --help Show this message and exit.
get_roles command¶
Usage:
parsec roles get_roles [OPTIONS]
Help
Displays a collection (list) of roles.
Output
- A list of dicts with details on individual roles.
For example:
[{"id": "f2db41e1fa331b3e", "model_class": "Role", "name": "Foo", "url": "/api/roles/f2db41e1fa331b3e"}, {"id": "f597429621d6eb2b", "model_class": "Role", "name": "Bar", "url": "/api/roles/f597429621d6eb2b"}]
Options:
-h, --help Show this message and exit.
show_role command¶
Usage:
parsec roles show_role [OPTIONS] ROLE_ID
Help
Display information on a single role
Output
- A description of role
For example:
{"description": "Private Role for Foo", "id": "f2db41e1fa331b3e", "model_class": "Role", "name": "Foo", "type": "private", "url": "/api/roles/f2db41e1fa331b3e"}
Options:
-h, --help Show this message and exit.
tool_data¶
This section is auto-generated from the help text for the parsec command
tool_data.
delete_data_table command¶
Usage:
parsec tool_data delete_data_table [OPTIONS] DATA_TABLE_ID VALUES
Help
Delete an item from a data table.
Output
Options:
-h, --help Show this message and exit.
get_data_tables command¶
Usage:
parsec tool_data get_data_tables [OPTIONS]
Help
Get the list of all data tables.
Output
- A list of dicts with details on individual data tables.
For example:
[{"model_class": "TabularToolDataTable", "name": "fasta_indexes"}, {"model_class": "TabularToolDataTable", "name": "bwa_indexes"}]
Options:
-h, --help Show this message and exit.
reload_data_table command¶
Usage:
parsec tool_data reload_data_table [OPTIONS] DATA_TABLE_ID
Help
Reload a data table.
Output
- A description of the given data table and its content.
For example:
{"columns": ["value", "dbkey", "name", "path"], "fields": [["test id", "test", "test name", "/opt/galaxy-dist/tool-data/test/seq/test id.fa"]], "model_class": "TabularToolDataTable", "name": "all_fasta"}
Options:
-h, --help Show this message and exit.
show_data_table command¶
Usage:
parsec tool_data show_data_table [OPTIONS] DATA_TABLE_ID
Help
Get details of a given data table.
Output
- A description of the given data table and its content.
For example:
{"columns": ["value", "dbkey", "name", "path"], "fields": [["test id", "test", "test name", "/opt/galaxy-dist/tool-data/test/seq/test id.fa"]], "model_class": "TabularToolDataTable", "name": "all_fasta"}
Options:
-h, --help Show this message and exit.
tools¶
This section is auto-generated from the help text for the parsec command
tools.
get_tool_panel command¶
Usage:
parsec tools get_tool_panel [OPTIONS]
Help
Get a list of available tool elements in Galaxy’s configured toolbox.
Output
- List containing tools (if not in sections) or tool sections
- with nested tool descriptions.
See also
bioblend.galaxy.toolshed.get_repositories()
Options:
-h, --help Show this message and exit.
get_tools command¶
Usage:
parsec tools get_tools [OPTIONS]
Help
Get all tools or filter the specific one(s) via the provided name or tool_id. Provide only one argument, name or tool_id, but not both.
Output
List of tool descriptions.See also
bioblend.galaxy.toolshed.get_repositories()
Options:
--tool_id TEXT id of the requested tool
--name TEXT name of the requested tool(s)
--trackster if True, only tools that are compatible with Trackster are
returned
-h, --help Show this message and exit.
install_dependencies command¶
Usage:
parsec tools install_dependencies [OPTIONS] TOOL_ID
Help
Install dependencies for a given tool via a resolver. This works only for Conda currently. This functionality is available since Galaxy release_16.10 and is available only to Galaxy admins.
Output
Options:
-h, --help Show this message and exit.
paste_content command¶
Usage:
parsec tools paste_content [OPTIONS] CONTENT HISTORY_ID
Help
Upload a string to a new dataset in the history specified by history_id.
Output
Options:
-h, --help Show this message and exit.
put_url command¶
Usage:
parsec tools put_url [OPTIONS] CONTENT HISTORY_ID
Help
Upload a string to a new dataset in the history specified by history_id.
Output
Options:
-h, --help Show this message and exit.
run_tool command¶
Usage:
parsec tools run_tool [OPTIONS] HISTORY_ID TOOL_ID TOOL_INPUTS
Help
Runs tool specified by tool_id in history indicated by history_id with inputs from dict tool_inputs.
Output
Options:
-h, --help Show this message and exit.
show_tool command¶
Usage:
parsec tools show_tool [OPTIONS] TOOL_ID
Help
Get details of a given tool.
Output
Options:
--io_details if True, get also input and output details
--link_details if True, get also link details
-h, --help Show this message and exit.
upload_file command¶
Usage:
parsec tools upload_file [OPTIONS] PATH HISTORY_ID
Help
Upload the file specified by path to the history specified by history_id.
Output
Options:
--dbkey TEXT (optional) genome dbkey
--file_name TEXT (optional) name of the new history dataset
--file_type TEXT Galaxy datatype for the new dataset, default is auto
--space_to_tab whether to convert spaces to tabs. Default is False.
Applicable only if to_posix_lines is True
--to_posix_lines if True, convert universal line endings to POSIX line
endings. Default is True. Set to False if you upload a gzip,
bz2 or zip archive containing a binary file
-h, --help Show this message and exit.
upload_from_ftp command¶
Usage:
parsec tools upload_from_ftp [OPTIONS] PATH HISTORY_ID
Help
Upload the file specified by path from the user’s FTP directory to the history specified by history_id.
Output
Options:
-h, --help Show this message and exit.
toolshed¶
This section is auto-generated from the help text for the parsec command
toolshed.
get_repositories command¶
Usage:
parsec toolshed get_repositories [OPTIONS]
Help
Get the list of all installed Tool Shed repositories on this Galaxy instance.
Options:
-h, --help Show this message and exit.
install_repository_revision command¶
Usage:
parsec toolshed install_repository_revision [OPTIONS] TOOL_SHED_URL NAME
Help
Install a specified repository revision from a specified Tool Shed into this Galaxy instance. This example demonstrates installation of a repository that contains valid tools, loading them into a section of the Galaxy tool panel or creating a new tool panel section. You can choose if tool dependencies or repository dependencies should be installed through the Tool Shed, (use install_tool_dependencies or install_repository_dependencies) or through a resolver that supports installing dependencies (use install_resolver_dependencies). Note that any combination of the three dependency resolving variables is valid.
Options:
--install_tool_dependencies Whether or not to automatically handle tool
dependencies (see
https://galaxyproject.org/toolshed/tool-
dependency-recipes/ for more details)
--install_repository_dependencies
Whether or not to automatically handle
repository dependencies (see
https://galaxyproject.org/toolshed/defining-
repository-dependencies/ for more details)
--install_resolver_dependencies
Whether or not to automatically install
resolver dependencies (e.g. conda). This
parameter is silently ignored in Galaxy
``release_16.04`` and earlier.
--tool_panel_section_id TEXT The ID of the Galaxy tool panel section where
the tool should be insterted under. Note that
you should specify either this parameter or
the ``new_tool_panel_section_label``. If both
are specified, this one will take precedence.
--new_tool_panel_section_label TEXT
The name of a Galaxy tool panel section that
should be created and the repository installed
into.
-h, --help Show this message and exit.
show_repository command¶
Usage:
parsec toolshed show_repository [OPTIONS] TOOLSHED_ID
Help
Get details of a given Tool Shed repository as it is installed on this Galaxy instance.
Options:
-h, --help Show this message and exit.
toolshed_categories¶
This section is auto-generated from the help text for the parsec command
toolshed_categories.
get_categories command¶
Usage:
parsec toolshed_categories get_categories [OPTIONS]
Help
Returns a list of dictionaries that contain descriptions of the repository categories found on the given Tool Shed instance.
Output
- A list of dictionaries containing information about
repository categories present in the Tool Shed. For example:
[{u'deleted': False, u'description': u'Tools for manipulating data', u'id': u'175812cd7caaf439', u'model_class': u'Category', u'name': u'Text Manipulation', u'url': u'/api/categories/175812cd7caaf439'}]New in version 0.5.2.
Options:
--deleted whether to show deleted categories
-h, --help Show this message and exit.
show_category command¶
Usage:
parsec toolshed_categories show_category [OPTIONS] CATEGORY_ID
Help
Get details of a given category.
Output
details of the given category
Options:
-h, --help Show this message and exit.
toolshed_repositories¶
This section is auto-generated from the help text for the parsec command
toolshed_repositories.
create_repository command¶
Usage:
parsec [OPTIONS] COMMAND [ARGS]...
Help
Create a new repository in a Tool Shed.
get_ordered_installable_revisions command¶
Usage:
parsec [OPTIONS] COMMAND [ARGS]...
Help
Returns the ordered list of changeset revision hash strings that are associated with installable revisions. As in the changelog, the list is ordered oldest to newest.
get_repositories command¶
Usage:
parsec [OPTIONS] COMMAND [ARGS]...
Help
Get a list of all the repositories in a Galaxy Tool Shed.
toolshed_tools¶
This section is auto-generated from the help text for the parsec command
toolshed_tools.
search_tools command¶
Usage:
parsec toolshed_tools search_tools [OPTIONS] Q
Help
Search for tools in a Galaxy Tool Shed.
Output
- dictionary containing search hits as well as metadata for the
search. For example:
{u'hits': [{u'matched_terms': [], u'score': 3.0, u'tool': {u'description': u'convert between various FASTQ quality formats', u'id': u'69819b84d55f521efda001e0926e7233', u'name': u'FASTQ Groomer', u'repo_name': None, u'repo_owner_username': u'devteam'}}, {u'matched_terms': [], u'score': 3.0, u'tool': {u'description': u'converts a bam file to fastq files.', u'id': u'521e282770fd94537daff87adad2551b', u'name': u'Defuse BamFastq', u'repo_name': None, u'repo_owner_username': u'jjohnson'}}], u'hostname': u'https://testtoolshed.g2.bx.psu.edu/', u'page': u'1', u'page_size': u'2', u'total_results': u'118'}
Options:
--page INTEGER page requested [default: 1]
--page_size INTEGER page size requested [default: 10]
-h, --help Show this message and exit.
users¶
This section is auto-generated from the help text for the parsec command
users.
create_local_user command¶
Usage:
parsec users create_local_user [OPTIONS] USERNAME USER_EMAIL PASSWORD
Help
Create a new Galaxy local user.
Output
a dictionary containing information about the created user
Options:
-h, --help Show this message and exit.
create_remote_user command¶
Usage:
parsec users create_remote_user [OPTIONS] USER_EMAIL
Help
Create a new Galaxy remote user.
Output
a dictionary containing information about the created user
Options:
-h, --help Show this message and exit.
create_user_apikey command¶
Usage:
parsec users create_user_apikey [OPTIONS] USER_ID
Help
Create a new API key for a given user.
Output
the API key for the user
Options:
-h, --help Show this message and exit.
delete_user command¶
Usage:
parsec users delete_user [OPTIONS] USER_ID
Help
Delete a user.
Output
a dictionary containing information about the deleted user
Options:
--purge if ``True``, also purge (permanently delete) the history
-h, --help Show this message and exit.
get_current_user command¶
Usage:
parsec users get_current_user [OPTIONS]
Help
Display information about the user associated with this Galaxy connection.
Output
a dictionary containing information about the current user
Options:
-h, --help Show this message and exit.
get_user_apikey command¶
Usage:
parsec users get_user_apikey [OPTIONS] USER_ID
Help
Get the current API key for a given user. This functionality is available since Galaxy release_17.01.
Output
the API key for the user
Options:
-h, --help Show this message and exit.
get_users command¶
Usage:
parsec users get_users [OPTIONS]
Help
Get a list of all registered users. If deleted is set to True, get a list of deleted users.
Output
- a list of dicts with user details.
For example:
[{u'email': u'a_user@example.com', u'id': u'dda47097d9189f15', u'url': u'/api/users/dda47097d9189f15'}]
Options:
--deleted TEXT
--f_email TEXT filter for user emails. The filter will be active for non-
admin users only if the Galaxy instance has the
``expose_user_email`` option set to ``True`` in the
``config/galaxy.ini`` configuration file. This parameter is
silently ignored for non-admin users in Galaxy
``release_15.01`` and earlier.
--f_name TEXT filter for user names. The filter will be active for non-admin
users only if the Galaxy instance has the ``expose_user_name``
option set to ``True`` in the ``config/galaxy.ini``
configuration file. This parameter is silently ignored in
Galaxy ``release_15.10`` and earlier.
--f_any TEXT filter for user email or name. Each filter will be active for
non-admin users only if the Galaxy instance has the
corresponding ``expose_user_*`` option set to ``True`` in the
``config/galaxy.ini`` configuration file. This parameter is
silently ignored in Galaxy ``release_15.10`` and earlier.
-h, --help Show this message and exit.
show_user command¶
Usage:
parsec users show_user [OPTIONS] USER_ID
Help
Display information about a user.
Output
a dictionary containing information about the user
Options:
--deleted whether to return results for a deleted user
-h, --help Show this message and exit.
utils¶
This section is auto-generated from the help text for the parsec command
utils.
cmp command¶
Usage:
parsec utils cmp [OPTIONS] METHOD CMP_WITH
Help
comparison tool. Exits if the value read from stdin does not pass the comparison test with the specified value.
method is the comparison method. One of these (lt, gt, eq, ne) which will trigger a numerical comparison (cast to floats), or one of teq, tneq which will trigger a string comparison.
cmp_with is the value to compare against. E.g. ‘100’ or ‘test’
e.g.:
echo '5' | parsec utils cmp lt 10 # exit 0
echo '5' | parsec utils cmp lt 1 # exit 1
Options:
-h, --help Show this message and exit.
library_recurse command¶
Usage:
parsec utils library_recurse [OPTIONS] LIBRARY_ID
Help
Get all the folders or filter specific one(s) via the provided name or folder_id in data library with id library_id. Provide only one argument: name or folder_id, but not both.
Output
list of dicts each containing basic information about a folder
Options:
--path TEXT Folder path to filter on (otherwise root of repo)
-h, --help Show this message and exit.
wait_on_invocation command¶
Usage:
parsec utils wait_on_invocation [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
Given a workflow and invocation id, wait until that invocation is complete (or one or more steps have errored)
This will exit with the following error codes:
- 0: done successfully
- 1: running (if –exit_early)
- 2: failure
- 3: unknown
Options:
--exit_early Exit immediately after checking status rather than
sleeping indefinitely
--backoff_min FLOAT Minimum time to sleep between checks, in seconds.
--backoff_max FLOAT Maximum time to sleep between checks, in seconds
-h, --help Show this message and exit.
xunit_xargs command¶
Usage:
parsec utils xunit_xargs [OPTIONS] _
Help
xargs look-alike that wraps output calls as XUnit XML
e.g.:
parsec histories get_histories | jq '.[].id' -r | head -n 3 | parsec utils xunit_xargs parsec histories get_status \| jq .percent_complete
will fetch the first three histories mentioned, and then pass them to xargs
to run parsec histories get_status [history_id] | jq .percent_complete. This will
in turn produce XUnit XML that can be used in Jenkins or similar systems:
<?xml version="1.0" ?>
<testsuites errors="0" failures="0" tests="3" time="1.5944418907165527">
<testsuite errors="0" failures="0" name="Parsec XX" skipped="0" tests="3" time="1.5944418907165527">
<testcase classname="parsec.histories.get_status.769f01a3981796db_|.jq..percent_complete" name="parsec.histories.get_status.769f01a3981796db_" time="0.604831">
<system-out>100</system-out>
</testcase>
<testcase classname="parsec.histories.get_status.83fbc32772cb5fcf_|.jq..percent_complete" name="parsec.histories.get_status.83fbc32772cb5fcf_" time="0.483556">
<system-out>100</system-out>
</testcase>
<testcase classname="parsec.histories.get_status.90c9282cb8718062_|.jq..percent_complete" name="parsec.histories.get_status.90c9282cb8718062_" time="0.506056">
<system-out>97.82608695652173</system-out>
</testcase>
</testsuite>
</testsuites>
Options:
-h, --help Show this message and exit.
visual¶
This section is auto-generated from the help text for the parsec command
visual.
get_visualizations command¶
Usage:
parsec visual get_visualizations [OPTIONS]
Help
Get the list of all visualizations.
Output
- A list of dicts with details on individual visualizations.
For example:
[{u'dbkey': u'eschColi_K12', u'id': u'df1c7c96fc427c2d', u'title': u'AVTest1', u'type': u'trackster', u'url': u'/api/visualizations/df1c7c96fc427c2d'}, {u'dbkey': u'mm9', u'id': u'a669f50f8bf55b02', u'title': u'Bam to Bigwig', u'type': u'trackster', u'url': u'/api/visualizations/a669f50f8bf55b02'}]
Options:
-h, --help Show this message and exit.
show_visualization command¶
Usage:
parsec visual show_visualization [OPTIONS] VISUAL_ID
Help
Get details of a given visualization.
Output
- A description of the given visualization.
For example:
{u'annotation': None, u'dbkey': u'mm9', u'id': u'18df9134ea75e49c', u'latest_revision': { ... }, u'model_class': u'Visualization', u'revisions': [u'aa90649bb3ec7dcb', u'20622bc6249c0c71'], u'slug': u'visualization-for-grant-1', u'title': u'Visualization For Grant', u'type': u'trackster', u'url': u'/u/azaron/v/visualization-for-grant-1', u'user_id': u'21e4aed91386ca8b'}
Options:
-h, --help Show this message and exit.
workflows¶
This section is auto-generated from the help text for the parsec command
workflows.
cancel_invocation command¶
Usage:
parsec workflows cancel_invocation [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
Cancel the scheduling of a workflow.
Output
Options:
-h, --help Show this message and exit.
delete_workflow command¶
Usage:
parsec workflows delete_workflow [OPTIONS] WORKFLOW_ID
Help
Delete a workflow identified by workflow_id.
Output
Options:
-h, --help Show this message and exit.
export_workflow_dict command¶
Usage:
parsec workflows export_workflow_dict [OPTIONS] WORKFLOW_ID
Help
Exports a workflow.
Output
Dictionary representing the requested workflow
Options:
-h, --help Show this message and exit.
export_workflow_json command¶
Usage:
parsec workflows export_workflow_json [OPTIONS] WORKFLOW_ID
Help
Deprecated since version 0.9.0: Use export_workflow_dict() instead.
Output
Options:
-h, --help Show this message and exit.
export_workflow_to_local_path command¶
Usage:
parsec workflows export_workflow_to_local_path [OPTIONS] WORKFLOW_ID
Help
Exports a workflow in JSON format to a given local path.
Output
Options:
--use_default_filename If the use_default_name parameter is True, the
exported file will be saved as file_local_path/Galaxy-
Workflow-%s.ga, where %s is the workflow name. If
use_default_name is False, file_local_path is assumed
to contain the full file path including filename.
[default: True]
-h, --help Show this message and exit.
get_invocations command¶
Usage:
parsec workflows get_invocations [OPTIONS] WORKFLOW_ID
Help
Get a list containing all the workflow invocations corresponding to the specified workflow.
Output
- A list of workflow invocations.
For example:
[{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'model_class': u'WorkflowInvocation', u'state': u'new', u'update_time': u'2015-10-31T22:00:22', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}]
Options:
-h, --help Show this message and exit.
get_workflow_inputs command¶
Usage:
parsec workflows get_workflow_inputs [OPTIONS] WORKFLOW_ID LABEL
Help
Get a list of workflow input IDs that match the given label. If no input matches the given label, an empty list is returned.
Output
list of workflow inputs matching the label query
Options:
-h, --help Show this message and exit.
get_workflows command¶
Usage:
parsec workflows get_workflows [OPTIONS]
Help
Get all workflows or filter the specific one(s) via the provided name or workflow_id. Provide only one argument, name or workflow_id, but not both.
Output
- A list of workflow dicts.
For example:
[{u'id': u'92c56938c2f9b315', u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}]
Options:
--workflow_id TEXT Encoded workflow ID (incompatible with ``name``)
--name TEXT Filter by name of workflow (incompatible with
``workflow_id``). If multiple names match the given name,
all the workflows matching the argument will be returned.
--published if ``True``, return also published workflows
-h, --help Show this message and exit.
import_workflow_dict command¶
Usage:
parsec workflows import_workflow_dict [OPTIONS] WORKFLOW_DICT
Help
Imports a new workflow given a dictionary representing a previously exported workflow.
Output
Options:
--publish if ``True`` the uploaded workflow will be published; otherwise it
will be visible only by the user which uploads it (default)
-h, --help Show this message and exit.
import_workflow_from_local_path command¶
Usage:
parsec workflows import_workflow_from_local_path [OPTIONS]
Help
Imports a new workflow given the path to a file containing a previously exported workflow.
Output
Options:
--publish if ``True`` the uploaded workflow will be published; otherwise it
will be visible only by the user which uploads it (default)
-h, --help Show this message and exit.
import_workflow_json command¶
Usage:
parsec workflows import_workflow_json [OPTIONS] WORKFLOW_JSON
Help
Deprecated since version 0.9.0: Use import_workflow_dict() instead.
Output
Options:
-h, --help Show this message and exit.
invoke_workflow command¶
Usage:
parsec workflows invoke_workflow [OPTIONS] WORKFLOW_ID
Help
Invoke the workflow identified by workflow_id. This will cause a workflow to be scheduled and return an object describing the workflow invocation.
Output
- A dict containing the workflow invocation describing the
scheduling of the workflow. For example:
{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'inputs': {u'0': {u'id': u'a7db2fac67043c7e', u'src': u'hda', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}}, u'model_class': u'WorkflowInvocation', u'state': u'ready', u'steps': [{u'action': None, u'id': u'd413a19dec13d11e', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 0, u'state': None, u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'cbbbf59e8f08c98c', u'workflow_step_label': None, u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485'}, {u'action': None, u'id': u'2f94e8ae9edff68a', u'job_id': u'e89067bb68bee7a0', u'model_class': u'WorkflowInvocationStep', u'order_index': 1, u'state': u'new', u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'964b37715ec9bd22', u'workflow_step_label': None, u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e'}], u'update_time': u'2015-10-31T22:00:26', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}The
paramsdict should be specified as follows:{STEP_ID: PARAM_DICT, ...}where PARAM_DICT is:
{PARAM_NAME: VALUE, ...}For backwards compatibility, the following (deprecated) format is also supported for
params:{TOOL_ID: PARAM_DICT, ...}in which case PARAM_DICT affects all steps with the given tool id. If both by-tool-id and by-step-id specifications are used, the latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also be specified as:
{'param': PARAM_NAME, 'value': VALUE}Note that this format allows only one parameter to be set per step.
The
replacement_paramsdict should map parameter names in post-job actions (PJAs) to their runtime values. For instance, if the final step has a PJA like the following:{u'RenameDatasetActionout_file1': {u'action_arguments': {u'newname': u'${output}'}, u'action_type': u'RenameDatasetAction', u'output_name': u'out_file1'}}then the following renames the output dataset to ‘foo’:
replacement_params = {'output': 'foo'}see also this email thread.
Warning
Historically, the
run_workflowmethod consumed adataset_mapdata structure that was indexed by unencoded workflow step IDs. These IDs would not be stable across Galaxy instances. The newinputsproperty is instead indexed by either theorder_indexproperty (which is stable across workflow imports) or the step UUID which is also stable.
Options:
--inputs TEXT A mapping of workflow inputs to datasets and
dataset collections. The datasets source can
be a LibraryDatasetDatasetAssociation
(``ldda``), LibraryDataset (``ld``),
HistoryDatasetAssociation (``hda``), or
HistoryDatasetCollectionAssociation
(``hdca``).
--params TEXT A mapping of non-datasets tool parameters (see
below)
--history_id TEXT The encoded history ID where to store the
workflow output. Alternatively,
``history_name`` may be specified to create a
new history.
--history_name TEXT Create a new history with the given name to
store the workflow output. If both
``history_id`` and ``history_name`` are
provided, ``history_name`` is ignored. If
neither is specified, a new 'Unnamed history'
is created.
--import_inputs_to_history If ``True``, used workflow inputs will be
imported into the history. If ``False``, only
workflow outputs will be visible in the given
history.
--replacement_params TEXT pattern-based replacements for post-job
actions (see below)
--allow_tool_state_corrections If True, allow Galaxy to fill in missing tool
state when running workflows. This may be
useful for workflows using tools that have
changed over time or for workflows built
outside of Galaxy with only a subset of inputs
defined.
-h, --help Show this message and exit.
run_invocation_step_action command¶
Usage:
parsec workflows run_invocation_step_action [OPTIONS] WORKFLOW_ID
Help
nature of this action and what is expected will vary based on the the type of workflow step (the only currently valid action is True/False for pause steps).
Output
Options:
-h, --help Show this message and exit.
run_workflow command¶
Usage:
parsec workflows run_workflow [OPTIONS] WORKFLOW_ID
Help
Run the workflow identified by workflow_id.
Output
- A dict containing the history ID where the outputs are placed
as well as output dataset IDs. For example:
{u'history': u'64177123325c9cfd', u'outputs': [u'aa4d3084af404259']}The
paramsdict should be specified as follows:{STEP_ID: PARAM_DICT, ...}where PARAM_DICT is:
{PARAM_NAME: VALUE, ...}For backwards compatibility, the following (deprecated) format is also supported for
params:{TOOL_ID: PARAM_DICT, ...}in which case PARAM_DICT affects all steps with the given tool id. If both by-tool-id and by-step-id specifications are used, the latter takes precedence.
Finally (again, for backwards compatibility), PARAM_DICT can also be specified as:
{'param': PARAM_NAME, 'value': VALUE}Note that this format allows only one parameter to be set per step.
The
replacement_paramsdict should map parameter names in post-job actions (PJAs) to their runtime values. For instance, if the final step has a PJA like the following:{u'RenameDatasetActionout_file1': {u'action_arguments': {u'newname': u'${output}'}, u'action_type': u'RenameDatasetAction', u'output_name': u'out_file1'}}then the following renames the output dataset to ‘foo’:
replacement_params = {'output': 'foo'}see also this email thread.
Warning
This method waits for the whole workflow to be scheduled before returning and does not scale to large workflows as a result. This method has therefore been deprecated in favor of
invoke_workflow(), which also features improved default behavior for dataset input handling.
Options:
--dataset_map TEXT A mapping of workflow inputs to datasets. The
datasets source can be a
LibraryDatasetDatasetAssociation (``ldda``),
LibraryDataset (``ld``), or
HistoryDatasetAssociation (``hda``). The map must
be in the following format: ``{'<input>': {'id':
<encoded dataset ID>, 'src': '[ldda, ld, hda]'}}``
(e.g. ``{'23': {'id': '29beef4fadeed09f', 'src':
'ld'}}``)
--params TEXT A mapping of non-datasets tool parameters (see
below)
--history_id TEXT The encoded history ID where to store the workflow
output. Alternatively, ``history_name`` may be
specified to create a new history.
--history_name TEXT Create a new history with the given name to store
the workflow output. If both ``history_id`` and
``history_name`` are provided, ``history_name`` is
ignored. If neither is specified, a new 'Unnamed
history' is created.
--import_inputs_to_history If ``True``, used workflow inputs will be imported
into the history. If ``False``, only workflow
outputs will be visible in the given history.
--replacement_params TEXT pattern-based replacements for post-job actions
(see below)
-h, --help Show this message and exit.
show_invocation command¶
Usage:
parsec workflows show_invocation [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
Get a workflow invocation object representing the scheduling of a workflow. This object may be sparse at first (missing inputs and invocation steps) and will become more populated as the workflow is actually scheduled.
Output
- The workflow invocation.
For example:
{u'history_id': u'2f94e8ae9edff68a', u'id': u'df7a1f0c02a5b08e', u'inputs': {u'0': {u'id': u'a7db2fac67043c7e', u'src': u'hda', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}}, u'model_class': u'WorkflowInvocation', u'state': u'ready', u'steps': [{u'action': None, u'id': u'd413a19dec13d11e', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 0, u'state': None, u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'cbbbf59e8f08c98c', u'workflow_step_label': None, u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485'}, {u'action': None, u'id': u'2f94e8ae9edff68a', u'job_id': u'e89067bb68bee7a0', u'model_class': u'WorkflowInvocationStep', u'order_index': 1, u'state': u'new', u'update_time': u'2015-10-31T22:00:26', u'workflow_step_id': u'964b37715ec9bd22', u'workflow_step_label': None, u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e'}], u'update_time': u'2015-10-31T22:00:26', u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c', u'workflow_id': u'03501d7626bd192f'}
Options:
-h, --help Show this message and exit.
show_invocation_step command¶
Usage:
parsec workflows show_invocation_step [OPTIONS] WORKFLOW_ID INVOCATION_ID
Help
See the details of a particular workflow invocation step.
Output
- The workflow invocation step.
For example:
{u'action': None, u'id': u'63cd3858d057a6d1', u'job_id': None, u'model_class': u'WorkflowInvocationStep', u'order_index': 2, u'state': None, u'update_time': u'2015-10-31T22:11:14', u'workflow_step_id': u'52e496b945151ee8', u'workflow_step_label': None, u'workflow_step_uuid': u'4060554c-1dd5-4287-9040-8b4f281cf9dc'}
Options:
-h, --help Show this message and exit.
show_workflow command¶
Usage:
parsec workflows show_workflow [OPTIONS] WORKFLOW_ID
Help
Display information needed to run a workflow.
Output
- A description of the workflow and its inputs.
For example:
{u'id': u'92c56938c2f9b315', u'inputs': {u'23': {u'label': u'Input Dataset', u'value': u''}}, u'name': u'Simple', u'url': u'/api/workflows/92c56938c2f9b315'}
Options:
-h, --help Show this message and exit.