From abbe282df27b75b9d14826a634de2f01968e6e1b Mon Sep 17 00:00:00 2001 From: Weishan Li Date: Thu, 2 Jan 2025 14:55:33 -0700 Subject: [PATCH 1/4] Added section on downloading data in README.md --- 0.download_data/README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/0.download_data/README.md b/0.download_data/README.md index b8bf8c6..477360c 100644 --- a/0.download_data/README.md +++ b/0.download_data/README.md @@ -2,3 +2,9 @@ In this module, we will add all relevant information for downloading the datasets (including images, XML files, platemaps, etc.) when it comes available. All platemaps and layout figures will be included under the [metadata](./metadata/) folder of this module. + +--- + +## Current Access Instructions for Miscroscopy Images (Development) + +**Note:** The current method of accessing and downloading the microscopy image data is intended for development purposes only. When the data becomes publicly available, access methods will change, and this README will be updated to reflect the final public access protocol. \ No newline at end of file From d53d2d6a0814ded53f3cb29407d50cc1c5dd1b42 Mon Sep 17 00:00:00 2001 From: Weishan Li Date: Thu, 2 Jan 2025 14:56:45 -0700 Subject: [PATCH 2/4] Added prerequisite and environment setup instructions for data download in README.md --- 0.download_data/README.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/0.download_data/README.md b/0.download_data/README.md index 477360c..4cdbf84 100644 --- a/0.download_data/README.md +++ b/0.download_data/README.md @@ -7,4 +7,14 @@ All platemaps and layout figures will be included under the [metadata](./metadat ## Current Access Instructions for Miscroscopy Images (Development) -**Note:** The current method of accessing and downloading the microscopy image data is intended for development purposes only. When the data becomes publicly available, access methods will change, and this README will be updated to reflect the final public access protocol. \ No newline at end of file +**Note:** The current method of accessing and downloading the microscopy image data is intended for development purposes only. When the data becomes publicly available, access methods will change, and this README will be updated to reflect the final public access protocol. + +--- + +### Pre-Requisites and Dependencies +- Access to CU-Boulder Alpine compute cluster. +- Access to PetaLibrary Data storage on the Alpine compute cluster (specifically `/pl/active/koala/`). +- A registered **Globus account** with CU credentials and access to the Globus web interface. + - *(Optional)* Installation of the `globus-cli` command-line tool for advanced users. +- Globus Connect Personal installed and configured on the local machine for data transfer. + - Ensure that the local Globus endpoint is properly configured with allowed paths for data transfer. \ No newline at end of file From 2df42614e1e301df54d3f087701352e630045454 Mon Sep 17 00:00:00 2001 From: Weishan Li Date: Thu, 2 Jan 2025 14:57:46 -0700 Subject: [PATCH 3/4] Added Globlus web interface instructions for data download in README.md --- 0.download_data/README.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/0.download_data/README.md b/0.download_data/README.md index 4cdbf84..e857038 100644 --- a/0.download_data/README.md +++ b/0.download_data/README.md @@ -17,4 +17,17 @@ All platemaps and layout figures will be included under the [metadata](./metadat - A registered **Globus account** with CU credentials and access to the Globus web interface. - *(Optional)* Installation of the `globus-cli` command-line tool for advanced users. - Globus Connect Personal installed and configured on the local machine for data transfer. - - Ensure that the local Globus endpoint is properly configured with allowed paths for data transfer. \ No newline at end of file + - Ensure that the local Globus endpoint is properly configured with allowed paths for data transfer. + +--- + +### Instructions for Data Transfer Using Globus Web Interface +1. Log in to the [Globus web interface](https://app.globus.org/). +2. Select the **File Manager** tab from the left-hand menu. +3. Search for the source and destination endpoints in the search box: + - Source endpoint: `CU Boulder Research Computing` for Alpine. + - Destination endpoint: your personal Globus Connect Personal endpoint. +4. Specify the source path (`/pl/active/koala/`) and the destination path on your local machine. + - Note: You must explicitly configure your Globus Connect Personal installation to allow access to the intended local paths. +5. Select the files to transfer and click **Start Transfer**. You can configure transfer options (e.g., email notifications, concurrency) under **Transfer & Timer Options**. +6. During the transfer, you may need to authorize access to both endpoints using your CU credentials. \ No newline at end of file From f33352e6e3942c1d9e53014b15bd389df6da86b6 Mon Sep 17 00:00:00 2001 From: Weishan Li Date: Fri, 3 Jan 2025 12:06:59 -0700 Subject: [PATCH 4/4] Added Globlus commandline client instructions for data download in README.md --- 0.download_data/README.md | 31 ++++++++++++++++++++++++++++++- 1 file changed, 30 insertions(+), 1 deletion(-) diff --git a/0.download_data/README.md b/0.download_data/README.md index e857038..635011c 100644 --- a/0.download_data/README.md +++ b/0.download_data/README.md @@ -30,4 +30,33 @@ All platemaps and layout figures will be included under the [metadata](./metadat 4. Specify the source path (`/pl/active/koala/`) and the destination path on your local machine. - Note: You must explicitly configure your Globus Connect Personal installation to allow access to the intended local paths. 5. Select the files to transfer and click **Start Transfer**. You can configure transfer options (e.g., email notifications, concurrency) under **Transfer & Timer Options**. -6. During the transfer, you may need to authorize access to both endpoints using your CU credentials. \ No newline at end of file +6. During the transfer, you may need to authorize access to both endpoints using your CU credentials. + +### Instructions for Data Transfer Using Globus CLI +1. Log in to the Globus CLI using the command `globus login`. + +2. Look up endpoint IDs: + - For Alpine, use the command `globus endpoint search "CU Boulder Research Computing"`. + * As of 01/02/2025, the endpoint ID for Alpine is `4718fe94-aafd-498a-8bae-6bd430bb50a0`. + - For your local machine, use the command `globus endpoint local-id`. + +3. Initiate the transfer: + - Use the command `globus transfer :/pl/active/koala/ :/local/path/to/destination`. + - Replace `` and `` with the appropriate endpoint IDs. + - Replace `` and `/local/path/to/destination` with the specific paths. + +4. Confirm the transfer: + - You may be prompted to authorize the transfer. Follow the on-screen instructions. + - After initiating the transfer, the console should output: + `Message: The transfer has been accepted and a task has been created and queued for execution` + `Task ID: xxxxx` + +5. Monitor the transfer: + - Use the command `globus task show ` to check the status of your transfer. + +--- + +### Future Access Information +Once the microscopy image data is publicly released, access will no longer require CU credentials or the current development-specific setup. Instructions for public access, including any associated data repositories, will be added here upon release. + +--- \ No newline at end of file