From 3eff6fe5e7fa46424f79203569ed3b425b2a5f17 Mon Sep 17 00:00:00 2001 From: Manish Kuniyal <110035752+manish0kuniyal@users.noreply.github.com> Date: Mon, 1 Jan 2024 23:44:48 +0530 Subject: [PATCH 1/3] Enhanced installation guide --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 29190bde..3892f474 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,9 @@ location. # Installation ## Installing with pip +Before installing the `ga4gh.vrs[extras]` package, ensure that **PostgreSQL** is installed on your system. You can download and install PostgreSQL from [here](https://www.postgresql.org/download/). + +Once PostgreSQL is installed, proceed with the following command to install the `ga4gh.vrs[extras]` package: pip install 'ga4gh.vrs[extras]' @@ -186,4 +189,4 @@ This implementation is offered as-is, and without any security guarantees. It will need an independent security review before it can be considered ready for use in security-critical applications. If you integrate this code into your application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security -audit. \ No newline at end of file +audit. From c1249a3dc14791cd06c4fa11810606dee5c3aad3 Mon Sep 17 00:00:00 2001 From: Manish Kuniyal <110035752+manish0kuniyal@users.noreply.github.com> Date: Tue, 2 Jan 2024 23:46:25 +0530 Subject: [PATCH 2/3] Added MacSetup and Postgres for UTA. --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 3892f474..66ed49be 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,8 @@ location. # Installation ## Installing with pip +Check out the Mac setup guide for vrs-python [here](https://github.com/ga4gh/vrs-python/blob/main/docs/setup_help/m1_mac_setup.md). This is a crucial step before diving into UTA. Once you've completed the setup, proceed with configuring the PostgreSQL database for the Unified Transcriptome Annotation (UTA) application [here](https://github.com/ga4gh/vrs-python/blob/main/docs/setup_help/uta_installation.md). + Before installing the `ga4gh.vrs[extras]` package, ensure that **PostgreSQL** is installed on your system. You can download and install PostgreSQL from [here](https://www.postgresql.org/download/). Once PostgreSQL is installed, proceed with the following command to install the `ga4gh.vrs[extras]` package: From 4e0426f17a4989c1854363ee2b2b4deaea2262ea Mon Sep 17 00:00:00 2001 From: Manish Kuniyal <110035752+manish0kuniyal@users.noreply.github.com> Date: Wed, 3 Jan 2024 12:51:26 +0530 Subject: [PATCH 3/3] Added Homebrew installation guide and referenced documentation --- README.md | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 66ed49be..7f8db435 100644 --- a/README.md +++ b/README.md @@ -93,9 +93,25 @@ location. # Installation ## Installing with pip -Check out the Mac setup guide for vrs-python [here](https://github.com/ga4gh/vrs-python/blob/main/docs/setup_help/m1_mac_setup.md). This is a crucial step before diving into UTA. Once you've completed the setup, proceed with configuring the PostgreSQL database for the Unified Transcriptome Annotation (UTA) application [here](https://github.com/ga4gh/vrs-python/blob/main/docs/setup_help/uta_installation.md). - -Before installing the `ga4gh.vrs[extras]` package, ensure that **PostgreSQL** is installed on your system. You can download and install PostgreSQL from [here](https://www.postgresql.org/download/). +Before installing the `ga4gh.vrs[extras]` package, ensure that **PostgreSQL** is installed on your system. You can download and install PostgreSQL from [here](https://www.postgresql.org/download/). +### To install PostgreSQL using ``Homebrew`` +1.**Install Homebrew**: If you don't have Homebrew installed, you can install it by opening Terminal and running the following command: +``` +/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" +``` +2.**Update Homebrew**: Make sure Homebrew is up-to-date by running: +``` +brew update +``` +3.**Install PostgreSQL**: Use the following command to install PostgreSQL: +``` +brew install postgresql +``` +4.**Start PostgreSQL**: Once the installation is complete, you can start the PostgreSQL service using: +``` +brew services start postgresql +``` +You can refer to these documents [setup help docs](https://github.com/ga4gh/vrs-python/tree/main/docs/setup_help) for additional assistance. Once PostgreSQL is installed, proceed with the following command to install the `ga4gh.vrs[extras]` package: @@ -179,7 +195,7 @@ We have created a public [`VRS-demo-notebooks`](https://app.terra.bio/#workspace [VS Code](https://code.visualstudio.com/) is a code editor developed by Microsoft. It is lightweight, highly customizable, and supports a wide range of programming languages, with a robust extension system. You can download VS Code [here](https://code.visualstudio.com/Download). **1. Open VS Code**: Launch Visual Studio Code. -**2. Install the Jupyter Extension**: Use Extensions view (Ctrl+Shift+X or ⌘+Shift+X) to install the [Jupyter extension](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter). +**2. Install the Jupyter Extension**: Use Extensions view (Ctrl+Shift+X or ⌘+Shift+X) to install the [Jupyter extension](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter). **3. Open the Project in VS Code**: Navigate to your project folder and open it in VS Code. **4. Select the Jupyter Kernel**: In a notebook, click `Select Kernel` at the top right. Select the option where the path is `venv/3.10/bin/python3`. See [here](https://code.visualstudio.com/docs/datascience/jupyter-kernel-management) for more information on managing Jupyter Kernels in VS Code. **5. Run the Notebook**: After selecting the kernel you can now run the notebook.