7th May 2024
- In "Installing the Desktop Agent for Linux", the command for adding the package-signing key has been corrected. Also added the instructions for installing the Agent package on the PromethION 2 Solo.
- In "EPI2ME updates", a note has been added: "If you use Linux and have installed EPI2ME via the command line, follow the installation instructions described in Installing the Desktop Agent for Linux to perform any updates."
1st December 2022
The "Working with datasets" section has been updated with new screenshots and some new information for EPI2ME Portal release v2.0.0. Added information includes: data security, stopping analysis from the report, new button for downloading datasets, changing the operating region in which the dataset is homed, and a new glossary of terms.
19th October 2022
- "The EPI2ME Agent" and "Starting data analysis" - a new screenshot of the workflow report has been added, with the text: "The report in the Agent also links to the Output directory, Analysis workflow documentation page, and the Input directory."
- "Networking" - the instructions for configuring a proxy have been updated.
- "Starting data analysis" - a new screenshot has been added for ending an analysis, with the text: "If you try to stop an analysis before a report has been generated, the Agent will also display a warning message. If you exit the analysis at this stage, you will not see a report for this analysis."
10th August 2022
- In "Starting data analysis", a new note has been added: "If you stop the workflow while one or more analyses are still running, the Agent will display a warning message before shutdown. If you exit the workflow at this stage, all active data uploads will stop."
- In "Working with datasets", a new set of instructions has been added for downloading a dataset
13th July 2022
In "The EPI2ME Portal", the screenshots and descriptions have been changed under "Clicking on the avatar presents several options for account management."
23rd February 2022
The "EPI2ME CLI" section has been re-written to describe the newly-released CLI Agent v3.3. The section is now split into "Installation", "Commands and help", and "Common usage examples".
26th January 2022
Updates for the EPI2ME Portal update to v1.1.3:
- In "Introduction - The EPI2ME Portal", information has been added about the new dataset feature
- In "Running data analysis", added a new step called "Working with datasets"
25th August 2021
Updates for the release of EPI2ME Agent v3.4.0:
"Introduction to EPI2ME":
- Updated links to the IT requirements for all devices
- Updated screenshots of the Settings page, the Analysis list and the Applications menu in the EPI2ME Agent
"Download and install the EPI2ME Desktop Agent":
- Updated screenshots for configuring a proxy
- Updated a screenshot for obtaining a registration code
- A new section for "Managing profiles" has been added
"Starting data analysis":
- Updated screenshots for the list of analysis options, and run-time parameters - this includes an explanation that the new default is to download no data or telemetry during the analysis
"CLI Agent":
- The link for obtaining the registration code has been changed to https://epi2me.nanoporetech.com/profile#reg
- The list of commands has changed
28th July 2021
In "CLI Agent", the instructions for registering the Commandline Agent for the first time have been updated to include setting a profile name:
"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."
23rd June 2021
- In "Introduction to EPI2ME", two new sub-sections have been added: "The EPI2ME portal" and "The EPI2ME Agent"
- All references to "EPI2ME website" have been changed to "EPI2ME portal"
- In "The EPI2ME portal", all screenshots and descriptions have been updated to reflect the new Portal re-design
- In "Download and install the EPI2ME Desktop Agent", the link to the Agent downloads page has changed to https://epi2me.nanoporetech.com/software
- The screenshot for obtaining an EPI2ME Agent registration key has been updated
- The section describing analysis workflows has been removed; detailed information about all EPI2ME workflows can now be found in the EPI2ME portal: https://epi2me.nanoporetech.com/workflows
24th March 2021
- In the "FASTQ WIMP (What's In My Pot)" step, the information under "Classification available in WIMP" has been changed to include the updated RefSeq database in the 2021.03.05 version of the analysis workflow
10th March 2021
- In the "Analysis workflows" section, added information about a new workflow, FASTQ ARTIC + Nextclade
- In the "Analysis workflows" section, "FASTQ 16S" step, added details of the new database of reference sequences for v2021.03.05 of the workflow
11th February 2021
Changes in line with the release of EPI2ME Agent v3.2.0:
- Added new "Networking" sections with instructions for configuring a proxy
- "Obtaining a registration code" section: new screenshots for UI prompts to enter a registration code and profile name
- New screenshots of analysis parameter page in "Starting data analysis", "FASTQ Barcoding", "FASTQ 16S", "FASTA reference upload", "FASTQ Custom Alignment" and "FASTQ SV Caller for Human" sections
- "Starting data analysis" section: updated instructions for submitting a bug report using the new application menu
Other changes:
- "FASTQ 16S" section: removed erroneous reference to a TSV file output
- "Installing the Desktop Agent for Ubuntu 16 and 18" section: updated the command for launching the Desktop Agent once it has been installed
23rd December 2020
- Removed the need to access IP address 106.187.40.102 in the __Installing the Desktop Agent for Windows and Mac OS X__ section.
- Updated EPI2ME Agent installation instructions on Ubuntu; the new command to install the Agent is `sudo apt-get install epi2me-agent3`, or `sudo apt-get install epi2me-agent3-gridion` for GridION, or `sudo apt-get install epi2me-agent3-promethion` for PromethION
12th Nov 2020
Changes in line with release of an update to the FASTA Reference Upload workflow (v2020.10.28):
- The upload file size limit has been increased to 8 Gbytes.
- The workflow can now process and index reference genomes that contain 1000s of scaffolds.
- Telemetry report will summarise the indexed sequence lengths for only the 1000 longest contigs or transcripts.
15th Oct 2020
Changes in line with release of EPI2ME Agent v3.0:
- Real-time report in the Agent
- Previous analysis can be accessed
- Multiple input file sources
- Run multiple workflows at the same time
- Improved data upload mechanisms
- 'Favourite' analysis workflows
22nd October 2019
Updates for v2019.9 of the Desktop Agent:
- An updated registration process, where the API key copy & paste is replaced with a timed registration code
- Users are now asked to confirm the location of the input data folder before starting a workflow
- The Agent prevents upload of files exceeding the upload file size limit set by a workflow (500 Mbytes for the FASTQ 16S workflow, 1 Gbyte for all other workflows)