EPI2ME平台

概览

EPI2ME的使用说明。 仅供研究使用

Document version: MTE_1014_v1_revCB_11Apr2016

1. 计算机配置要求

The EPI2ME platform

The EPI2ME platform (created by Metrichor Ltd., a subsidiary of Oxford Nanopore Technologies) offers a number of workflows for end-to-end analysis of nanopore data.

In a typical experiment, the user would prepare a DNA or RNA library for sequencing on a nanopore sequencing device. The sequencing experiment is started from the MinKNOW software, which controls the device and translates the electrical signals from each DNA/RNA read into basecalled sequences. The sequences for each read are saved in the .fast5 or FASTQ file format.

The basecalled FASTQ files can then be uploaded to the EPI2ME platform via a piece of software called the EPI2ME Agent. The user selects a workflow in the Agent such as 16S alignment, and the Agent transfers the read files one by one into the cloud for real-time analysis.

The analysis results are generated and updated in real-time in the form of a report in the EPI2ME platform.

Data flow EPI2ME

2. The EPI2ME portal

The EPI2ME portal provides access to a variety of information about real-time analysis of nanopore sequencing data.

Users can navigate to the EPI2ME portal from https://epi2me.nanoporetech.com to manage profile information, account details, and access their analysis reports and datasets.

The Dashboard displays analyses that have been run by, or shared with the user.

Dashboard

Clicking on Open report displays the analysis report and information about the run:

Open report

A list of the current workflows is available under the Workflows tab.

Workflows

The Quick view button shows the workflow version and some basic details.

WIMP quick view

Clicking Learn more ... opens up a detailed description of the workflow, with links to an example report, example datasets, citations and Nanopore Community release notes.

WIMP learn more

New releases of the Desktop and CLI Agents are available on the Software page:

Software

Datasets can be managed and analysed in the Datasets tab.

Screenshot 2022-01-21 at 16.06.37

There are three types of datasets:

  • Source: the raw data uploaded to EPI2ME. Every time you upload files to EPI2ME for analysis, a Source dataset will be created.
  • Output: files/sequences/metadata produced during each discrete step of an analysis. For example, there will be a separate dataset created for the barcoding step, and another one for e.g. metagenomic classification.
  • Reference: a special type of output produced by the FASTA Reference Upload workflow that can be used as reference sequence database for custom alignment analysis.

Output source reference

All datasets are temporarily available to view from the Analysis page while the analysis is running. After the analysis is complete, you have the option of saving the dataset to the EPI2ME cloud indefinitely. Only datasets that are stored in EPI2ME can be viewed in the Dataset dashboard. Storage of datasets in EPI2ME is optional and free, but may incur extra costs in future.

Datasets not stored in EPI2ME will be deleted from the platform (whichever is first):

Clicking Go to dataset opens a more detailed view and allows dataset management:

  • Sharing the dataset with other EPI2ME users
  • Storing the dataset in the cloud
  • Reusing the dataset for a new analysis in EPI2ME
  • Deleting the dataset

Screenshot 2022-01-21 at 16.07.40

representative-ouput-dataset-full-page

Clicking on the avatar presents several options for account management.

4eb936f4-e1d4-4d92-82d3-f39b008a58cc

The Profile tab shows the user's details and the API keys.

Profile

Account details allows you to view the full list of people associated with an account, and to enable or disable sharing of analysis reports and datasets between participants.

Account details

Ask the Community takes you to the Nanopore Community, where you can ask questions and get support with your sequencing experiments.

Operating region allows you to switch between different operating regions. Screenshot 2022-07-13 at 13.34.03

3. The EPI2ME Agent

The EPI2ME Agent is a cross-platform desktop application for executing data analyses within the EPI2ME platform.

The EPI2ME Agent communicates with the EPI2ME platform API over secure https both to execute analyses and to transfer data files in and out. The Agent is configured using a user's credentials for the platform to enforce security access controls. The Agent also has rudimentary capabilities for filtering returned files post-analysis.

The Agent is also available as a command-line-only option.

The CLI Agent can be downloaded from https://epi2me.nanoporetech.com/software

Desktop Agent homepage

When installing the EPI2ME Agent for the first time, a registration must be entered on the home page. The registration code is obtained from the EPI2ME website and is needed to validate the user.

Agent registration link

Once the code has been entered successfully, the New analysis tab becomes clickable and an analysis can be started.

Homepage new analysis

Settings

The Settings page shows the profile that is currently in use, and information about the data input/output folders, network, and the version of the Agent.

Screenshot 2021-08-18 at 09.06.01

Screenshot 2021-03-19 at 16.47.31

Analysis

The appropriate analysis for the experiment can be chosen and run from the Analysis list.

Screenshot 2021-08-17 at 10.34.57

Analysis parameters

In this section, the user can configure the analysis parameters.

Screenshot 2020-11-25 at 21.05.40

Screenshot 2020-11-25 at 21.06.26

Running an analysis

Once the initialisation is complete, the Agent will begin securely uploading sequence data into the EPI2ME portal. The analysis begins as soon as the first batch of sequence data is successfully uploaded. A subset of the analysis report can be viewed either in the Agent itself, or the full report can be viewed by clicking the View report button (enabled only when reports are available), which directs the user to the EPI2ME portal.

If data is uploaded in batches, the report will be updated periodically to enable users to monitor the progress of the analysis in real-time.

Analysis in progress

The analysis can be stopped at any time with the Stop upload button to only stop file upload, or Stop analysis to stop both file upload and analysis.

The Upload/download progress section will display the amount of already-uploaded data and number of files and reads that have been uploaded.

Once a report becomes available, it is shown as a summary in the Agent. A more detailed report is available from the EPI2ME portal.

Report

The report in the Agent also links to the Output directory, Analysis workflow documentation page, and the Input directory.

image-20221003-110424

报错

如果桌面代理或者数据分析出现任何问题,您可点击界面上的报错图标(红框所示)发送报告给我们。

Bug report icon

Bug Report CN

4. 在Windows和Mac OS X上安装桌面代理

EPI2ME和桌面代理

经过碱基识别的序列数据通过桌面代理(亦称“EPI2ME代理”)在主机和EPI2ME分析流程之间进行交换。为下载桌面代理,您首先需要建立一个EPI2ME账户。建立账户时,您将需要: (1) 为每位用户单独生成的注册码;该注册码由字母和数字组成。 (2) EPI2ME网站的账户登录信息——即您用来登录纳米孔社区(Nanopore Community)的邮箱和密码。

运行MinION Mk1B的防火墙设置

在运行期间,MinKNOW和桌面代理都需要访问列在此处的、由亚马逊网络服务公司 (AWS)提供的eu-west-1区域的IP地址范围;并同时需要访问:

178.79.175.200

96.126.99.215

106.187.40.102

浏览 https://epi2me.nanoporetech.com

单击此链接导航至该网站。

点击“Log In” (登入),输入您在纳米孔社区所使用的电邮地址和密码。

进入纳米孔社区“软件下载”板块,然后根据您所使用的操作系统下载最新版本的软件。

  • 选择“Download”(下载)选项卡。
  • 选择适合您的操作系统的EPI2ME桌面代理。
  • 按照界面上的说明,安装桌面快捷方式。
  • 安装完成后,在“Desktop Agent Setup“(桌面代理安装)对话框上单击”Close”(关闭)。
步骤结束

您电脑桌面上出现的桌面代理图标标志着安装成功。

5. 在Ubuntu 16和18上安装桌面代理

打开命令行界面。

添加存储库:

对于Ubuntu 16,输入:

echo "deb http://mirror.oxfordnanoportal.com/apt xenial-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list

对于Ubuntu 18,输入:

echo "deb http://mirror.oxfordnanoportal.com/apt bionic-stable non-free" | sudo tee /etc/apt/sources.list.d/nanoporetech.sources.list

添加软件包签名密钥:

wget -O- https://mirror.oxfordnanoportal.com/apt/ont-repo.pub | sudo apt-key add -
可选操作

清除软件包索引:

sudo apt-get clean

更新软件包索引:

sudo apt-get update
可选操作

如需更新桌面代理,安装软件包:

sudo apt-get install epi2me-agent

安装软件包:

sudo apt-get install epi2me-agent

运行桌面代理:

/opt/metrichor/MetrichorAgent

6. EPI2ME更新

更新方法

  • 如登陆EPI2ME网站(http://epi2me.nanoporetech.com),您可在“Dowloads(下载)”页面找到最新软件。
  • 如遇重大更新,桌面代理启动时会弹出提示。您只有在下载最新版本后,才能继续使用此代理。
    

Critical update

Critical Update CN

如非重大更新,请留意桌面代理的“setting”(设置)页。

Agent update Settings

Agent Update CN

点击“Download new Agent" (点击新的桌面代理)或”Update“(更新)按钮

当软件提示有更新时,请访问 https://epi2me.nanoporetech.com 并登录EPI2ME账户。

关闭在主机上打开的所有EPI2ME代理界面。

点击EPI2ME网站的”Downloads“(下载)选项卡,下载与您操作系统匹配的最新版本的软件。

运行安装程序。

如果该下载包被杀毒软件屏蔽,请与您本地的IT管理员联系。

点击桌面快捷方式打开桌面代理。

7. Networking

To configure a proxy, navigate to the Settings page and click the "Manual proxy settings" option. Then enter the hostname or IP address.

image-20221003-122219

  1. Select the Proxy mode.
  2. Select the protocol: use the default setting or https if you are unsure.
  3. Specify the hostname and IP address of the proxy server. If you have a full URL for the proxy, you can paste it into the Host field. This will extract the protocol and port into the respective fields.
  4. Specify the port: use the default port if are unsure.
  5. Toggle Use proxy to ON.

8. 获取注册码

EPI2ME代理

EPI2ME代理(即桌面代理)是一款能直接从文件夹中调取文件并展开工作的独立应用程序。它的使用不受MinKNOW™测序限制(即从测序开始到结束后均可使用);使用过程中亦无需与MinION连接。在正式使用Epi2ME之前,您需要使用Oxford Nanopore Technologies的账户信息登陆EPI2ME网站,以激活账户。

在浏览器中启用弹出通知。

打开EPI2ME代理。您可以先浏览功能简介,再点击”Continue"(开始分析);或直接点击“Skip”(略过)。

Loading Combined
Ready to start analysis Combined

如果提示您获取注册码,请单击界面上的EPI2ME网站链接。

Registration Code CN

复制注册码。

Agent Screen 2 CN

将注册码粘贴到EPI2ME代理界面上的“REG CODE”(注册码)对话框中,点击”Register“(注册)。

Profile description

在"Profile description"(用户资料)中设定您在EPI2ME上的用户名。

您可以为不同用户分别创建资料。

点击“Register”(注册)。

步骤结束

您可开始使用EPI2ME代理。

9. Managing profiles

Profile information can be accessed by clicking the "Profile" button in the top right corner of the Agent.

Multiple profiles can be associated with one account. You can switch to a different profile by clicking Use profile next to your profile of choice, or create a new one by clicking the Create profile button.

Screenshot 2021-08-17 at 10.30.29

Profile options

Clicking on a profile box presents the options to either use the profile for the next EPI2ME analysis, or to delete the profile.

Screenshot 2021-08-17 at 10.32.39

Note: Exercise caution in deleting profiles, as this action cannot be undone.

Screenshot 2021-08-17 at 10.32.13

10. 开始数据分析

通过桌面快捷方式打开EPI2ME代理。

点击“New Analysis”(新的分析流程)选项。

Homepage new analysis

如有需要,请选择包含待分析FASTQ文件的文件夹。

“__EXPERIMENTS & SAMPLES__”(实验及样本)栏目下会列出在默认输入路径中检测到的、由MinKNOW生成的文件夹结构。您可以在“Settings”(设置)(齿轮图标)页面的“__Data sources__”(数据源)板块更改输入路径(input folder)。您亦可在”Settings”页面更改输出文件夹的根目录(output folder)。任何经分析流程得出的结果(以实例ID命名)都将被存储在该根目录下的输出文件夹内。您也可在设定分析流程参数时再更改输出文件夹根目录的地址。

Settings icon

或者,您可以在“__Folders__”(文件夹)栏目下选择所需的输入文件夹。

Selection Folder CN

选择您想运行的分析流程。

您既可以从所有的工作流程(All 选项)中选取所需的分析流程,也可以在被标记为“偏好”(Favourites 选项)的分析流程中进行选择。不同用户可独立设置其所偏好的分析流程。

Choose analysis

设定分析流程中的运行参数。

可调整的参数类型取决于所选择的分析流程。 Confirm yes human

Start Analysis Parameter CN1
Confirm2

Start Analysis Parameter CN2

当所有必需信息设定完成后,点击“Accept & start”(接受并开始)以启动数据分析。

在代理界面跟进序列文件的上传和下载进度。

Analysis in progress

Analysis in progress CN

点击“View report”(查看数据)跳转至EPI2ME网站。 代理界面上也会显示该报告的简化版本。

代理界面上的颜色(红框所示)可反映分析进程:

  • 绿色: 正在上传序列片段
  • 黄色: 正在分析数据
  • 蓝色: 可查看报告

Report EN

Report CN

当下载数据与上传数据量一致时,数据交换完成。点击“Stop upload”(停止上传)选项将仅停止工作流程中文件的上传;点击“Stop analysis”(停止分析)选项将同时停止文件的上传和下载。

经过分析的序列片段会被保存到“Setting”(设置)页面上设定的输出文件夹。

报错

如果桌面代理或者数据分析出现任何问题,您可点击界面上的报错图标(红框所示)发送报告给我们。

Bug report icon

Bug Report CN

11. Working with datasets

Introduction

You are able to store, manage, reanalyse and download data in the EPI2ME platform using the EPI2ME Data Manager. The EPI2ME Data Manager is a collection of web-based tools, services and interfaces that allow easy management of data associated with analyses uploaded to and run on the EPI2ME platform.

To create a new analysis, you need to provide Oxford Nanopore sequence files generated by the MinKNOW software as input and select an EPI2ME workflow. EPI2ME workflows are composed of several steps. Each step represents a logical unit of computation and/or analysis. Sequence data uploaded to the EPI2ME platform progress from one step to the next until all data have been processed (or you stop the analysis). The output of each step comprises one or more files that might include metadata, reference data, alignments (BAM), taxonomic classifications, basecalled sequences, etc. The files uploaded to EPI2ME and the collection of files output by each step of the workflow are each represented in EPI2ME as a reusable, sharable “Dataset”. Datasets are made available and managed in the EPI2ME Portal interface.

Data security

The EPI2ME platform is accredited to the ISO/IEC 27001 standard and your data will be encrypted in transit and at rest from the moment it is uploaded to the moment it is finally deleted. Datasets will not be stored in EPI2ME unless explicitly requested by the data owner. Datasets not explicitly stored are removed in accordance with our data retention policy. For full details about the security of your data in EPI2ME, please refer to our information governance document.

Location of datasets in EPI2ME Portal interface

Datasets are accessed and managed from the data manager on the EPI2ME Portal website - a collection of tools and interfaces that allow you to store and manage files uploaded to EPI2ME or the collection of files that are output by each step of a workflow. You can view your own and shared datasets from the Datasets tab in the Portal:

Screenshot 2023-03-30 at 13.43.18

All datasets are temporarily available to view from the Analysis page while the analysis is running. After the analysis is complete, you have the option of saving the dataset to the EPI2ME cloud indefinitely. Only datasets that are stored in EPI2ME can be viewed in the Dataset dashboard. Storage of datasets in EPI2ME is optional and free but may incur extra costs in future.

Datasets not stored in EPI2ME will be deleted from the platform (whichever is first):

Datasets can also be deleted at any time.

There are three types of datasets:

  • Source: the raw data uploaded to EPI2ME. Every time you upload files to EPI2ME for analysis, a Source dataset will be created.
  • Output: files/sequences/metadata produced during each discrete step of an analysis. For example, there will be a separate dataset created for the barcoding step, and another one for e.g. metagenomic classification.
  • Reference: a special type of output produced by the FASTA Reference Upload workflow that can be used as reference sequence database for custom alignment analysis.

Output source reference

Each dataset is represented by a tile with several items of information on it:

Screenshot 2022-01-21 at 16.07.40

  • Dataset type: Source, Output or Reference - described above
  • Workflow name: the workflow run in EPI2ME which created the dataset
  • Analysis: link to the analysis report
  • Tags: these are entered during analysis set-up in the EPI2ME Agent, and can be edited in the Portal
  • Created: the date on which the dataset was created
  • Size: this changes dynamically as data is uploaded into EPI2ME or is analysed
  • Stored in cloud or Expiring: if the dataset has not been permanently saved, it will be marked as "Expiring" until it is automatically deleted. Saved datasets are marked as "Stored in cloud"
  • Owner: the person who ran the workflow that generated the dataset

Clicking Go to dataset takes you to a new page with further information about the dataset, and options for dataset management:

image-20230330-132750

There are several ways to manage a dataset:

Screenshot 2023-03-30 at 13.52.36

  • Share the dataset with all other EPI2ME users (including users outside of one's own account)
  • Re-use the dataset for a new analysis in EPI2ME
  • Store the dataset in the cloud
  • Copy the dataset to another EPI2ME-enabled region
  • Download the dataset contents
  • Delete the dataset

Starting new analyses with datasets as input

Only datasets that are saved in EPI2ME can be reused to launch new analyses. Your data is uploaded to the EPI2ME platform once, then as new versions of software become available or new analysis workflows are released, you can re-analyse your data by running new workflows on your existing datasets. The choice of which analysis users are able to run is restricted to those analyses that are compatible with the dataset and its contents.

Setting up a new analysis from a dataset in the Portal mimics the analysis set-up in the EPI2ME Agent:

Screenshot 2022-01-21 at 16.56.55

Screenshot 2022-01-21 at 16.57.38

Please be aware that EPI2ME operates in multiple geographic regions, and analyses can only be run from datasets within the same EPI2ME-enabled operating region.

Important note: analyses can be stopped from within the Portal before completion, and users will be presented with an option to optionally store temporary datasets:

Screenshot 2022-01-21 at 16.51.18

However, old versions of the EPI2ME Agent do not offer this functionality, and stopping an analysis in the Agent will automatically delete datasets in the EPI2ME portal. To mitigate this, you will need to indicate in the Portal which datasets are to be stored, before stopping the analysis either in Portal or in the Desktop Agent.

Switching to other EPI2ME-enabled regions

To switch to another EPI2ME-enabled region you can either change the preferred Operating region from the profile menu or you can change your preferred Operating region in your user profile by clicking the blue profile button > Profile option > Operating region option.

Screenshot 2023-03-30 at 13.27.06

Copying datasets to/from other EPI2ME-enabled regions

In order to copy an existing dataset to or from other regions, you will first have to ensure that:

  1. You have the appropriate access to view and manage the selected dataset.
  2. The analysis that generated the dataset has been stopped.
  3. The dataset of interest has been stored in the EPI2ME platform.

The actions panel for a dataset will change depending on whether that dataset is stored in your current operating region. If the dataset is in your region then you will have access to a number of actions on that dataset including a new Copy dataset to button. However, if the operating region is different to that of the dataset you will be presented with the simpler actions panel and a Copy dataset here button. Below compare the two different routes whereby you will be able to copy datasets into other operating regions.

If the dataset is in the current operating region

Screenshot 2023-03-30 at 13.52.36

Click Copy dataset to:

Screenshot 2023-03-30 at 13.59.41

Dataset copy successfully finished:

Screenshot 2023-03-30 at 14.06.17

If the dataset is outside the current operating region

Screenshot 2023-03-30 at 13.54.09

Click Copy dataset here:

Screenshot 2023-03-30 at 13.55.43

Dataset copy successfully finished:

Screenshot 2023-03-30 at 13.57.15

The location of datasets including where they have been copied will be shown in the dataset details section of the page.

If a dataset is available in the current operating region, the region label will be emphasised in bold.

Screenshot 2023-03-30 at 14.11.25

Datasets can contain a very large number of files and the process of copying them into other regions will take time. You will be notified through the EPI2ME notification system when all files have been successfully copied after which the usual actions (Start analysis, download, share etc.) will become available.

Screenshot 2023-03-30 at 14.13.41

Deleting datasets from EPI2ME-enabled regions

If you have copied a dataset into other EPI2ME-enabled regions, you will be presented the option of which operating region you would like to delete datasets from. To begin deleting datasets, click on Delete dataset. You will then be presented with a panel with the various copies (replicas) listed. Datasets that are still in the process of being copied cannot be deleted and are distinguished by a Currently replicating label. As with the dataset details, the dataset that is in the current operating region is emphasised in bold. Select the dataset replicas you want to delete and click Delete replicas.

Screenshot 2023-03-30 at 14.21.31

Glossary of terms

EPI2ME: A cloud-based bioinformatics and analytics platform developed by Metrichor Ltd. EPI2ME Portal: A web portal in which users can view and manage data held in EPI2ME. Data manager: The collection of tools services and interfaces for managing the output of EPI2ME workflows. Dataset: A collection of files and folders representing the analysis output of each discrete step in an EPI2ME workflow. Reference dataset: A dataset created by running the FASTA Reference Upload workflow that can be used in custom reference alignment workflows as the reference data.

12. 命令行代理:安装及运行

命令行(CLI)代理简介

命令行代理通过命令行、而非用户界面,操控纳米孔分析。它囊括了桌面代理的全部功能,并可在Unix, Mac OS X, Linux和MS Windows系统上运作。命令行代理通过服务器端操作,无需用户界面,分析自主,并支持多项分析在一台电脑上同时运行。

访问 https://epi2me.nanoporetech.com,并使用您的单点登录(Single Sign-On)邮箱和密码进行登录。

点击”Downloads“(下载)选项卡,并在”Cli“(命令行代理)板块下载所需文件。

Click the "Download Command-line Agent" button to initiate the download.

Software download

解压缩下载文件。

例如: unzip epi2me-cli-macos-2019.11.11-2920621.zip

Create a profile (interactive mode, preferred)

Run the following using the Command-line Agent:

./epi2me-3.0.0-6800812 profiles register

And follow the steps that will guide you through the registration process.

可选操作

访问 https://epi2me.nanoporetech.com/reg 。

Navigate to https://epi2me.nanoporetech.com/profile#reg and copy the registration code:

agent registration

Use the code to register the device. You can also set a profile name, which results in a profile stored in the <USER HOME>/.epi2me.json file that can be used in both the Desktop Agent and CLI. For example:

./epi2me-3.0.0-6800812 profiles register a08fa8 --name CLI_DEMO

重要

Please note that if you have already registered a Desktop Agent, you will not need to register the CLI Agent.

13. Commands and help

From Command-line Agent v3.0.1 onwards, operation of the software is based around the syntax of commands. Each command encapsulates a specific behaviour and accepts a different set of options. Each of the commands also includes its own help text explaining what it does, what options it accepts and what they are used for.

Commands are composed in the format <epi2me-binary-name> CATEGORY ACTION. For example (assuming the binary has been renamed to epi2me):

epi2me workflows list

will display a list of workflows, and

epi2me workflows run

will execute a specified workflow.

There are seven categories related to the EPI2ME platform:

  • accounts - View the accounts associated with the current user
  • datasets - View and download datasets
  • instances - Get the telemetry for a workflow instance
  • products - View products, create new products and add workflows to products
  • profiles - View, edit and create EPI2ME profiles
  • settings - View and modify the configuration of the local application and your user account
  • workflows - View workflows and start new instances

In addition, there are two utility categories relating to the application itself:

  • version - Display the software version
  • help - Display help

Accessing help

Help is available at every level of the application and is accessed by adding the keyword help at the end of any command. Help has the general form:

  • <epi2me-binary-name> help
  • <epi2me-binary-name> CATEGORY help
  • <epi2me-binary-name> CATEGORY ACTION help

Example of ACTION help:

> ./epi2me-3.0.0-6800812 workflows detail help Get the details of a workflow

USAGE: epi2me workflows detail [options] [arg1]

EXAMPLES: epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs

COMMANDS: help Display help version Display version

OPTIONS: --apikey An apikey to use for authentication instead of a profile. Must be used with a apisecret. --apisecret An apisecret to use for authentication instead of a profile. Must be used with a apikey. --docs Print the documentation for the workflow, if it exists. --h, --help Output usage information --product ID of the product to use. --profile The name of a local user profile to use for authentication. --proxy Address of a network proxy to use. --quiet Disable interactive prompts and omit supplementary output. --region The region to run the given command in. --v, --version Output the version number --workflow ID of the workflow to use.

Example of CATEGORY help:

> ./epi2me-3.0.0-6800812 workflows help View workflows and start new instances

USAGE: epi2me workflows [options] [command]

EXAMPLES: epi2me workflows epi2me workflows list epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs epi2me workflows favourite epi2me workflows favourite $WORKFLOW_ID epi2me workflows unfavourite epi2me workflows unfavourite $WORKFLOW_ID

COMMANDS: detail Get the details of a workflow favourite Favourite a workflow help Display help list List all the available workflows run Start a new analysis unfavourite Unfavourite a workflow version Display version

OPTIONS: -h, --help Output usage information -v, --version Output the version number

Example of APPLICATION help:

> ./epi2me-3.0.0-6800812 help USAGE: epi2me [options] [command]

EXAMPLES: epi2me accounts epi2me accounts list epi2me datasets epi2me datasets list epi2me datasets detail epi2me datasets detail $DATASET_ID epi2me datasets download epi2me datasets download $DATASET_ID epi2me datasets download $DATASET_ID $DESTINATION_FOLDER epi2me profiles epi2me profiles list epi2me profiles register epi2me profiles register $REGISTRATION_CODE epi2me profiles register $REGISTRATION_CODE --name $PROFILE_NAME epi2me profiles delete epi2me profiles delete $PROFILE_NAME epi2me profiles rename epi2me profiles rename $OLD_PROFILE_NAME epi2me profiles rename $OLD_PROFILE_NAME $NEW_PROFILE_NAME epi2me instances epi2me instances list epi2me instances detail epi2me instances detail $INSTANCE_ID epi2me products epi2me products list epi2me products workflows epi2me products workflows $PRODUCT_ID epi2me settings epi2me settings get region epi2me settings get disablePrompts epi2me settings get profile epi2me settings get admin epi2me settings get proxy epi2me settings get analytics epi2me settings change region epi2me settings change region $REGION_NAME epi2me settings change disablePrompts $DISABLE_PROMPTS epi2me settings change profile epi2me settings change profile $PROFILE_NAME epi2me settings change admin $IS_ADMIN epi2me settings change proxy $PROXY epi2me settings change analytics $ENABLE_ANALYTICS epi2me settings list epi2me workflows epi2me workflows list epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N epi2me workflows detail epi2me workflows detail $WORKFLOW_ID epi2me workflows detail $WORKFLOW_ID --docs epi2me workflows favourite epi2me workflows favourite $WORKFLOW_ID epi2me workflows unfavourite epi2me workflows unfavourite $WORKFLOW_ID

COMMANDS: accounts View the accounts associated with the current user datasets View and download datasets help Display help instances Get the telemetry for a workflow instance products View products, create new products and add workflows to products profiles View, edit and create epi2me profiles settings View and modify the configuration of the local application and your user account version Display version workflows View workflows and start new instances

OPTIONS: -h, --help Output usage information -v, --version Output the version number

14. Common usage examples

Below are some examples of common actions that can be carried out via the Command-line Agent.

List available accounts

epi2me accounts list

Describe a workflow (show details):

epi2me workflows detail $WORKFLOW_ID

Run new analysis (interactive mode)

This is analogous to starting a new analysis in EPI2ME where the user is interactively led through the process. The command to run in interactive mode takes the following form:

epi2me workflows run $INPUT_1 ... $INPUT_N

Here is a screenshot of a new analysis that was started interactively where the user is able to modify the settings at every step as they would in the Desktop Agent:

interactive run

Run new analysis (non-human data and accept defaults)

  • Multiple data sources as input
  • Data sources contain no human data

epi2me workflows run $INPUT_1 ... $INPUT_N --nothuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER

Run new analysis (human data with project tagging and opt-in storage. Accept defaults for the rest)

epi2me workflows run $INPUT_1 ... $INPUT_N --consentedHuman --workflow $WORKFLOW_ID --account $ACCOUNT_NUMBER --output $OUTPUT_LOCATION --store --quiet

Last updated: 10/7/2024

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