Seqera

https://docs.seqera.io/
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### Seqera CLI Installation and Setup

Source: https://docs.seqera.io/platform-enterprise/25.1/cli/installation

Commands to download, make executable, and move the Seqera CLI binary to a directory in the system's PATH. This ensures the CLI is accessible from any terminal session.

```bash
mv tw-* tw
chmod +x ./tw
sudo mv tw /usr/local/bin/
```

--------------------------------

### Seqera CLI Installation and Setup

Source: https://docs.seqera.io/platform-enterprise/23.4/cli/installation

Steps to download, make executable, and move the Seqera CLI binary to the system's PATH. This involves using `mv` to rename the downloaded file and `chmod` to grant execute permissions, followed by `sudo mv` to place it in a directory listed in the `$PATH`.

```Shell
mv tw-* tw
chmod +x ./tw
sudomv tw /usr/local/bin/
```

--------------------------------

### Install Nextflow

Source: https://docs.seqera.io/fusion/get-started

Command to install Nextflow on your system. This is a prerequisite for using Fusion with Nextflow pipelines.

```Shell
curl get.nextflow.io |bash
```

--------------------------------

### Use Access Token with Command Flag

Source: https://docs.seqera.io/platform-cloud/cli/installation

Example of providing the Seqera Platform access token directly via a command-line flag.

```bash
tw --access-token=<your access token><other options>
```

--------------------------------

### Download Example Data

Source: https://docs.seqera.io/multiqc/getting_started/quick_start

Downloads example data for RNA-seq analysis using curl and then unzips it to prepare for MultiQC processing.

```Shell
curl -O -J -L http://multiqc.info/examples/rna-seq/data.zip
unzip data.zip
```

--------------------------------

### Install and Configure Seqera CLI

Source: https://docs.seqera.io/platform-enterprise/cli/installation

Steps to download, make executable, and move the Seqera CLI binary to a directory in your PATH.

```bash
mv tw-* tw
chmod +x ./tw
sudo mv tw /usr/local/bin/
```

--------------------------------

### Install GraalVM

Source: https://docs.seqera.io/platform-cloud/cli/installation

Installs GraalVM using SDKMan, ensuring the tower-cli project's specific `.sdkmanrc` configuration is used for the installation.

```Bash
sdk envinstall  

```

--------------------------------

### Install GraalVM

Source: https://docs.seqera.io/platform-enterprise/cli/installation

Installs GraalVM using SDKMan, ensuring the tower-cli project's specific configuration is used.

```bash
sdk envinstall  
```

--------------------------------

### Verify Seqerakit Installation and Configuration

Source: https://docs.seqera.io/platform-enterprise/23.4/seqerakit/installation

Confirms that Seqerakit is installed correctly, the Platform CLI is configured, and the connection to Seqera is established. This command provides basic information about the setup.

```bash
seqerakit --info
```

--------------------------------

### Install GraalVM

Source: https://docs.seqera.io/platform-enterprise/23.4/cli/installation

Installs GraalVM using SDKMan, ensuring the tower-cli project's specific configuration is used.

```bash
sdk envinstall  
```

--------------------------------

### Seqera CLI Installation and Permissions

Source: https://docs.seqera.io/platform-enterprise/24.2/cli/installation

Steps to download the Seqera CLI binary, rename it, and make it executable. This is a fundamental step for using the CLI on your system.

```Shell
mv tw-* tw
chmod +x ./tw
```

```Shell
sudomv tw /usr/local/bin/
```

--------------------------------

### Install native-image

Source: https://docs.seqera.io/platform-enterprise/cli/installation

Installs the native-image component of GraalVM, which is necessary for creating native executables.

```bash
gu install native-image  
```

--------------------------------

### Check MultiQC Version

Source: https://docs.seqera.io/multiqc/getting_started/quick_start

Verifies the MultiQC installation by printing its version number.

```Shell
multiqc --version
```

--------------------------------

### Nextflow: Pre-run Script - Executor Setup Example

Source: https://docs.seqera.io/platform-enterprise/launch/advanced

Example pre-run script to add a delay for executor setup, allowing time for connectivity testing before Nextflow processes begin.

```bash
sleep 3600
```

--------------------------------

### Install MultiQC using Conda

Source: https://docs.seqera.io/multiqc/getting_started/quick_start

Installs the MultiQC tool within the active Conda environment using the bioconda channel.

```Bash
conda install multiqc
```

--------------------------------

### Nextflow Pre-run Script Examples

Source: https://docs.seqera.io/platform-cloud/launch/advanced

Examples of pre-run scripts for Nextflow. This includes updating Nextflow to a specific version and setting environment variables for executor setup or troubleshooting.

```bash
nextflow self-update
export NXF_VER=24.10.0
```

```bash
sleep 3600
```

--------------------------------

### Get Seqerakit Help Information

Source: https://docs.seqera.io/platform-cloud/seqerakit/installation

Displays a list of available commands and options for Seqerakit, providing guidance on its usage.

```Shell
seqerakit --help
```

--------------------------------

### Fix: Mention Tower Workspace ID Setup in Get Started

Source: https://docs.seqera.io/platform-cloud/cloud/changelog

A fix in 21.06.1 involves mentioning how to set up the Tower workspace ID in the 'Get started' page. This improves documentation and user onboarding.

--------------------------------

### Update Nextflow

Source: https://docs.seqera.io/fusion/get-started

Command to update an existing Nextflow installation to the latest version. This ensures you have the necessary features for Fusion integration.

```Shell
nextflow -self-update
```

--------------------------------

### Download and Make Executable

Source: https://docs.seqera.io/platform-cloud/cli/installation

Steps to download the Seqera CLI binary, rename it, and make it executable.

```bash
mv tw-* tw
chmod +x ./tw
```

--------------------------------

### Display Seqerakit Help Information

Source: https://docs.seqera.io/platform-enterprise/24.2/seqerakit/installation

Displays a list of all available Seqerakit commands and their options using the '--help' or '-h' flag. This provides a quick reference for using the tool.

```Bash
seqerakit --help
```

--------------------------------

### Seqera CLI with Custom SSL Certificate Authority

Source: https://docs.seqera.io/platform-enterprise/24.2/cli/installation

How to use a custom Java truststore for SSL certificates not recognized by default. This is useful for private CA setups.

```Shell
tw -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password> info
```

```Shell
#!/usr/bin/env bash
tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password>$@
```

--------------------------------

### Seqera Self-hosted Git Credentials Setup

Source: https://docs.seqera.io/platform-enterprise/23.4/git/overview

Information on configuring Seqera Platform Enterprise to support self-hosted Git server endpoints. Refer to the Enterprise installation guide for detailed Git configuration.

```text
Seqera Platform Enterprise supports Git server endpoints. For more information, see Git configuration in the Enterprise installation guide.
```

--------------------------------

### Display Seqerakit Help Information

Source: https://docs.seqera.io/platform-enterprise/25.1/seqerakit/installation

Shows a list of all available commands and their options for the Seqerakit CLI. This is the primary way to discover Seqerakit's capabilities.

```Bash
seqerakit --help
```

--------------------------------

### Seqera Self-hosted Git Credentials Setup

Source: https://docs.seqera.io/platform-enterprise/23.3/git/overview

Information on configuring Seqera Platform Enterprise to support self-hosted Git server endpoints. Refer to the Enterprise installation guide for detailed Git configuration.

```text
Seqera Platform Enterprise supports Git server endpoints. For more information, see Git configuration in the Enterprise installation guide.
```

--------------------------------

### Configure Fusion in Nextflow

Source: https://docs.seqera.io/fusion/get-started

Configuration snippet to be added to the `nextflow.config` file to enable Fusion and Wave. Requires replacing `<PLATFORM_ACCESS_TOKEN>` with your actual token.

```Groovy
fusion.enabled =true
wave.enabled =true
tower.accessToken ='<PLATFORM_ACCESS_TOKEN>'
```

--------------------------------

### Display Seqerakit Help Information

Source: https://docs.seqera.io/platform-enterprise/23.4/seqerakit/installation

Lists all available commands and their options for Seqerakit. This command is essential for understanding the full capabilities of the tool.

```bash
seqerakit --help
```

```bash
seqerakit -h
```

--------------------------------

### Install native-image

Source: https://docs.seqera.io/platform-enterprise/23.4/cli/installation

Installs the native-image component of GraalVM, which is necessary for creating native executables.

```bash
gu install native-image  
```

--------------------------------

### Seqera Platform CLI Installation

Source: https://docs.seqera.io/platform-enterprise/24.2/tags/installation

This snippet details the installation process for the Seqera Platform CLI. It outlines the steps required to download and set up the command-line tool for interacting with the Seqera Platform.

```Bash
# Example installation command (actual command may vary)
curl -fsSL https://get.seqera.io/cli | bash

```

--------------------------------

### Seqera Platform CLI Installation

Source: https://docs.seqera.io/platform-enterprise/tags/installation

This snippet details the process of installing the Seqera Platform CLI. It covers the necessary steps and any prerequisites for a successful installation.

```Bash
# Example installation command (actual command may vary)
sudo apt-get update && sudo apt-get install seqera-cli
```

--------------------------------

### Install Nextflow

Source: https://docs.seqera.io/fusion/guide

Command to install Nextflow if it is not already installed. This is a prerequisite for using Fusion with Nextflow.

```bash
curl get.nextflow.io |bash
```

--------------------------------

### Install native-image

Source: https://docs.seqera.io/platform-enterprise/25.1/cli/installation

Installs the 'native-image' component of GraalVM, which is necessary for compiling Java applications into native executables.

```Shell
gu install native-image  
```

--------------------------------

### Install native-image

Source: https://docs.seqera.io/platform-enterprise/24.2/cli/installation

Installs the 'native-image' component of GraalVM, which is necessary for compiling Java applications into native executables.

```Shell
gu install native-image  
```

--------------------------------

### Azure CLI Commands for Batch Setup

Source: https://docs.seqera.io/platform-enterprise/enterprise/advanced-topics/manual-azure-batch-setup

This snippet outlines the Azure CLI commands and steps required to set up an Azure Batch compute environment. It includes creating a storage account, a blob container for Nextflow, and configuring the Batch account with specific quota increases for EDv5 series, active jobs, pools, and spot/low-priority vCPUs.

```Bash
az storage account create --name <your-storage-account-name> --resource-group <your-resource-group> --location <your-region> --sku Standard_LRS
az storage container create --name work --account-name <your-storage-account-name>
az batch account create --name <your-batch-account-name> --resource-group <your-resource-group> --location <your-region> --storage-account <your-storage-account-name>

# Request Quota Increase (example values, adjust as needed)
az batch account set --name <your-batch-account-name> --resource-group <your-resource-group> --location <your-region> --max-jobs 100 --max-pools 50 --max-vms-per-pool 192 --max-vms-all-pools 192
```

--------------------------------

### Install native-image

Source: https://docs.seqera.io/platform-cloud/cli/installation

Installs the 'native-image' component of GraalVM, which is required for compiling Java applications into native executables.

```Bash
gu install native-image  

```

--------------------------------

### Seqera Platform CLI Configuration

Source: https://docs.seqera.io/platform-enterprise/24.2/tags/installation

This snippet covers the configuration steps for the Seqera Platform CLI after installation. It explains how to set up necessary credentials and parameters to connect to your Seqera Platform instance.

```Bash
# Example configuration command (actual command may vary)
seqera config set --api-key YOUR_API_KEY --endpoint YOUR_ENDPOINT

```

--------------------------------

### Compile Native Client

Source: https://docs.seqera.io/platform-enterprise/23.4/cli/installation

Compiles the native client using the Gradle wrapper script. This process generates the executable binary.

```gradle
./gradlew nativeCompile  
```

--------------------------------

### Nextflow Parameter Schema Example

Source: https://docs.seqera.io/platform-enterprise/25.1/getting-started/quickstart-demo/launch-pipelines

Demonstrates the structure of a `nextflow_schema.json` file used to define pipeline parameters for Seqera Platform. This schema allows for easy adaptation of Nextflow pipelines.

```json
{
  "name": "rnaseq",
  "description": "A Nextflow pipeline for RNA-Seq analysis.",
  "version": "3.15.1",
  "params": [
    {
      "name": "input",
      "type": "file",
      "description": "Path to the input samplesheet.",
      "required": true
    },
    {
      "name": "outdir",
      "type": "string",
      "description": "Directory for pipeline output.",
      "required": true
    },
    {
      "name": "genome",
      "type": "string",
      "description": "Reference genome assembly.",
      "default": "GRCh38"
    }
  ]
}
```

--------------------------------

### Display Seqerakit Help

Source: https://docs.seqera.io/platform-enterprise/seqerakit/installation

Shows the help message for Seqerakit, listing all available commands and their options. This is accessed using the --help or -h flag.

```Shell
seqerakit --help
```

--------------------------------

### Get Build Status with cURL

Source: https://docs.seqera.io/wave/api

This example shows how to retrieve the status of a specific build using its buildId. The endpoint returns details such as the build's ID, current status (PENDING or COMPLETED), start time, duration, and success status.

```bash
% curl --location 'http://localhost:9090/v1alpha1/builds/6c084f2e43f86a78_1/status'
```

--------------------------------

### Signal Workflow Execution Start - API Example

Source: https://docs.seqera.io/platform-api/info/trace-info

Provides examples for signaling the start of a workflow execution via the Seqera Platform API. This is crucial for tracking the lifecycle of pipeline runs.

```Bash
curl -X PUT https://api.seqera.io/v1/workspaces/{workspaceId}/workflows/{workflowId}/trace/start \
  -H "Authorization: Bearer YOUR_API_TOKEN"
```

```Python
import requests

api_url = "https://api.seqera.io/v1/workspaces/{workspaceId}/workflows/{workflowId}/trace/start"
headers = {
    "Authorization": "Bearer YOUR_API_TOKEN"
}

response = requests.put(api_url, headers=headers)
print(response.status_code)
```

```Java
import okhttp3.*;
import java.io.IOException;

public class WorkflowTraceStart {
    public static void main(String[] args) throws IOException {
        OkHttpClient client = new OkHttpClient();

        Request request = new Request.Builder()
            .url("https://api.seqera.io/v1/workspaces/{workspaceId}/workflows/{workflowId}/trace/start")
            .header("Authorization", "Bearer YOUR_API_TOKEN")
            .put(RequestBody.create(null, new byte[0])) // PUT request with empty body
            .build();

        try (Response response = client.newCall(request).execute()) {
            System.out.println(response.code());
        }
    }
}
```

--------------------------------

### Seqera Platform Launch Nextflow Hello World Pipeline

Source: https://docs.seqera.io/platform-cloud/enterprise/advanced-topics/manual-azure-batch-setup

This describes how to launch the 'nextflow-hello' pipeline from the Seqera Platform Launchpad. It involves selecting the previously configured Azure Batch compute environment, specifying the pipeline URL, and defining a work directory within Azure Storage.

```Seqera Platform Configuration
Add a pipeline from your workspace Launchpad with the following settings:
  * Select your Azure Batch compute environment from the dropdown.
  * For **Pipeline to launch** , enter `https://github.com/nextflow-io/hello`.
  * For **Work directory** , enter a subdirectory in the `az://work` container in your Storage account.
```

--------------------------------

### Install GraalVM with SDKMan!

Source: https://docs.seqera.io/platform-enterprise/25.1/cli/installation

Installs GraalVM using SDKMan! to ensure the tower-cli project's .sdkmanrc configuration is utilized for the build.

```Shell
sdk envinstall  
```

--------------------------------

### Seqera Platform CLI Configuration

Source: https://docs.seqera.io/platform-enterprise/tags/installation

This snippet outlines the configuration steps required after installing the Seqera Platform CLI. It typically involves setting up authentication and connection parameters.

```Bash
# Example configuration command (actual command may vary)
seqera config set --api-key YOUR_API_KEY --endpoint https://api.seqera.io
```

--------------------------------

### Install GraalVM with SDKMan!

Source: https://docs.seqera.io/platform-enterprise/24.2/cli/installation

Installs GraalVM using SDKMan! to ensure the tower-cli project's .sdkmanrc configuration is utilized for the build.

```Shell
sdk envinstall  
```

--------------------------------

### Get Seqerakit Version

Source: https://docs.seqera.io/platform-cloud/seqerakit/installation

Retrieves the currently installed version of the Seqerakit package.

```Shell
seqerakit --version
```

--------------------------------

### Verify Seqerakit Installation and Configuration

Source: https://docs.seqera.io/platform-enterprise/24.2/seqerakit/installation

Runs the 'seqerakit --info' command to verify that Seqerakit is installed correctly, the Platform CLI is configured, and the connection to Seqera is established. This is equivalent to running 'tw info'.

```Bash
seqerakit --info
```

--------------------------------

### Install Wave CLI with Homebrew

Source: https://docs.seqera.io/wave/cli/installation

Installs the latest version of the Wave CLI using the Homebrew package manager. This command adds the Seqera Labs tap and installs the `wave-cli` package.

```shell
brew install seqeralabs/tap/wave-cli
```

--------------------------------

### Install MultiQC on FreeBSD (From Source)

Source: https://docs.seqera.io/multiqc/getting_started/installation

Builds and installs MultiQC from source on FreeBSD by navigating to the port directory and running 'make install'.

```Shell
cd /usr/ports/biology/py-multiqc
make install
```

--------------------------------

### Launch Pipeline via Platform API

Source: https://docs.seqera.io/platform-cloud/getting-started/quickstart-demo/automation

This example demonstrates how to launch a pipeline using the Seqera Platform's public API. It requires an authentication token and specifies pipeline details like compute environment, run name, pipeline name, working directory, and revision.

```Bash
curl -X POST "https://api.cloud.seqera.io/workflow/launch?workspaceId=38659136604200" \
    -H "Accept: application/json" \
    -H "Authorization: Bearer <ACCESS_TOKEN>" \
    -H "Content-Type: application/json" \
    -H "Accept-Version:1" \
    -d '{  
    "launch": {  
        "computeEnvId": "hjE97A8TvD9PklUb0hwEJ",  
        "runName": "first-time-pipeline-api-byname",  
        "pipeline": "first-time-pipeline",  
        "workDir": "s3://nf-ireland",  
        "revision": "master"  
    }  
}'
```

--------------------------------

### Health Check Command

Source: https://docs.seqera.io/platform-cloud/cli/installation

Command to check the installation, configuration, and connection status of the Seqera CLI.

```bash
tw info
```

--------------------------------

### Verify Seqerakit Installation and Configuration

Source: https://docs.seqera.io/platform-enterprise/23.3/seqerakit/installation

Commands to verify that Seqerakit is installed correctly, the Platform CLI is configured, and the connection to Seqera is established. Includes commands to check info, version, and help.

```Bash
seqerakit --info
```

```Bash
seqerakit --version
```

```Bash
seqerakit -v
```

```Bash
seqerakit --help
```

```Bash
seqerakit -h
```

--------------------------------

### Azure CLI Commands for Setup

Source: https://docs.seqera.io/platform-cloud/enterprise/advanced-topics/manual-azure-batch-setup

This snippet demonstrates essential Azure CLI commands for setting up an Azure Batch compute environment. It includes creating a storage account, a blob container for Nextflow, and a Batch account. It also covers requesting quota increases for specific compute series and resource limits.

```Bash
az storage account create --name <your-storage-account-name> --resource-group <your-resource-group> --location <your-region> --sku Standard_LRS
az storage container create --name work --account-name <your-storage-account-name>
az batch account create --name <your-batch-account-name> --resource-group <your-resource-group> --location <your-region> --storage-account <your-storage-account-name>

# Request quota increase (example for EDv5 series)
az provider register -p Microsoft.Batch
az batch account set --resource-group <your-resource-group> --name <your-batch-account-name> --subscription <your-subscription-id>
az batch account quota-request create --account-name <your-batch-account-name> --location <your-region> --quota-name "total-cores" --value 192
az batch account quota-request create --account-name <your-batch-account-name> --location <your-region> --quota-name "pools" --value 50
az batch account quota-request create --account-name <your-batch-account-name> --location <your-region> --quota-name "jobs" --value 100
```

--------------------------------

### Install Seqerakit via Pip

Source: https://docs.seqera.io/platform-enterprise/25.1/seqerakit/installation

Installs the Seqerakit Python package using pip. This is the primary method for users who have Python and the Seqera Platform CLI already installed. It ensures you get the latest stable version from PyPI.

```Bash
pip install seqerakit
```

--------------------------------

### Verify Seqerakit Installation

Source: https://docs.seqera.io/platform-cloud/seqerakit/installation

Runs a command to confirm that Seqerakit is installed correctly, the Platform CLI is configured, and the connection to Seqera is established.

```Shell
seqerakit --info
```

--------------------------------

### Install Seqerakit via Pip

Source: https://docs.seqera.io/platform-enterprise/24.2/seqerakit/installation

Installs the Seqerakit Python package using pip. This is the primary method for users who have Python and the Seqera Platform CLI already installed. It ensures you get the latest stable version from PyPI.

```Bash
pip install seqerakit
```

--------------------------------

### Get Seqerakit Version

Source: https://docs.seqera.io/platform-enterprise/23.4/seqerakit/installation

Retrieves the currently installed version of Seqerakit. This is useful for checking compatibility or troubleshooting.

```bash
seqerakit --version
```

```bash
seqerakit -v
```

--------------------------------

### Launch Nextflow Pipeline

Source: https://docs.seqera.io/platform-cloud/getting-started/overview

This snippet outlines the general steps to launch a Nextflow pipeline from the Seqera Launchpad. It details selecting a pipeline, configuring input datasets, specifying output directories, and setting up notifications and reports.

```text
1. From the Launchpad, select a pipeline to view the pipeline detail page. _nf-core-rnaseq_ is a good first pipeline example.
2. Optional: Select the URL under **Workflow repository** to view the pipeline code repository in another tab.
3. Select **Launch** from the pipeline detail page.
4. On the **Launch pipeline** page, enter a unique **Workflow run name** or use the pre-filled random name.
5. Optional: Enter labels to be assigned to the run in the **Labels** field.
6. Under **Input/output options** , select the dataset named after your chosen pipeline from the drop-down menu under **input**.
7. Under **outdir** , specify an output directory where run results will be saved. This must be an absolute path to storage on cloud infrastructure and defaults to `./results`.
8. Under **email** , enter an email address where you wish to receive the run completion summary.
9. Under **multiqc_title** , enter a title for the MultiQC report. This is used as both the report page header and filename.

Once you've filled the necessary launch form details, select **Launch**. Your new run will be displayed at the top of the list in the **Runs** tab with a **submitted** status. Select the run name to navigate to the run detail page and view the configuration, parameters, status of individual tasks, and run report.
```

--------------------------------

### Get Seqerakit Version

Source: https://docs.seqera.io/platform-enterprise/25.1/seqerakit/installation

Retrieves the currently installed version of Seqerakit. This is useful for checking compatibility or reporting issues.

```Bash
seqerakit --version
```

--------------------------------

### Docker Compose Infrastructure Recommendations

Source: https://docs.seqera.io/platform-cloud/getting-started/production-checklist

Specifies recommended instance and database sizes for deploying Seqera Platform using Docker Compose. These are starting points, and resource needs can change based on pipeline activity.

```text
Instance size - `c5.2xlarge`
External DB Aurora V3 provisioned - `db.t3.medium`
External Redis - `cache.t2.micro`
```

--------------------------------

### Install Azcopy Start Task

Source: https://docs.seqera.io/platform-enterprise/compute-envs/azure-batch

This Bash command is used as a start task for Azure Batch VMs to install and prepare 'azcopy' for use. It makes the 'azcopy' executable and copies it to the shared directory on the node, making it available for subsequent tasks, such as staging files.

```Bash
bash-c"chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/"
```

--------------------------------

### Install Azcopy Start Task

Source: https://docs.seqera.io/platform-enterprise/24.2/compute-envs/azure-batch

This Bash command is used as a start task in Azure Batch to install `azcopy` on each VM joining the pool. It makes the `azcopy` executable and copies it to the shared directory on the node, making it available for use in subsequent tasks for file staging.

```Bash
bash-c"chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/"  
```

--------------------------------

### Seqera CLI Wrapper Script with Custom SSL

Source: https://docs.seqera.io/platform-enterprise/cli/installation

Create a wrapper script for the Seqera CLI binary to automatically include custom SSL certificate authority settings.

```bash
#!/usr/bin/env bash
tw-binary -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts -Djavax.net.ssl.trustStorePassword=<your-password>$@
```

--------------------------------

### Seqera CLI Command with Access Token Flag

Source: https://docs.seqera.io/platform-enterprise/cli/installation

Provide the Seqera access token directly to the CLI command using the --access-token flag.

```bash
tw --access-token=<your access token><other options>
```

--------------------------------

### Get Seqerakit Version

Source: https://docs.seqera.io/platform-enterprise/seqerakit/installation

Retrieves the current version of the installed Seqerakit package using the --version or -v flag.

```Shell
seqerakit --version
```

--------------------------------

### Install and Load R Packages

Source: https://docs.seqera.io/platform-enterprise/23.4/getting-started/rnaseq

Installs and loads essential R packages for RNA-Seq analysis, including BiocManager, limma, edgeR, ggplot2, and gplots. Ensure BiocManager is installed before proceeding.

```R
# Install required packages  
if(!requireNamespace("BiocManager", quietly = TRUE))  
  install.packages("BiocManager")  
BiocManager::install(c("limma","edgeR","ggplot2","gplots"))  
  
# Load required libraries  
library(limma)  
library(edgeR)  
library(ggplot2)  
library(gplots)  


```

--------------------------------

### Install AWS CLI v2

Source: https://docs.seqera.io/platform-cloud/enterprise/advanced-topics/manual-aws-batch-setup

Installs AWS CLI v2 by downloading and extracting a tarball, setting up the PATH, and creating a symbolic link to the aws binary. It also configures system settings for dirty bytes and starts/enables the Docker and ECS services.

```bash
mkdir -p /home/ec2-user
curl -s https://nf-xpack.seqera.io/miniconda-awscli/miniconda-awscli.tar.gz \
|tar xz -C /home/ec2-user
export PATH=$PATH:/home/ec2-user/miniconda/bin
ln -s /home/ec2-user/miniconda/bin/aws /usr/bin/aws

systemctl start docker
systemctl enable --now --no-block ecs
echo "1258291200" > /proc/sys/vm/dirty_bytes
echo "629145600" > /proc/sys/vm/dirty_background_bytes

runcmd:
  - bash /root/custom-ce.sh
```

--------------------------------

### Install Azcopy Start Task

Source: https://docs.seqera.io/platform-enterprise/25.1/compute-envs/azure-batch

This Bash command is used as a start task in Azure Batch to install `azcopy` on each VM joining the pool. It makes the `azcopy` executable and copies it to the shared directory on the node, making it available for use in subsequent tasks for file staging.

```Bash
bash-c"chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/"  
```

--------------------------------

### Seqera CLI Configuration: Access Token

Source: https://docs.seqera.io/platform-enterprise/24.2/cli/installation

Instructions on how to configure the Seqera CLI with an access token, either by exporting it as an environment variable or by passing it as a command-line flag.

```Shell
exportTOWER_ACCESS_TOKEN=<your access token>
```

```Shell
tw --access-token=<your access token><other options>
```

--------------------------------

### Install Azcopy Start Task

Source: https://docs.seqera.io/platform-cloud/compute-envs/azure-batch

This Bash command is used as a start task in Azure Batch to install `azcopy` on each VM joining the pool. It makes the `azcopy` executable and copies it to the shared directory on the node, making it available for use in subsequent tasks for file staging.

```Bash
bash-c"chmod +x azcopy && mkdir $AZ_BATCH_NODE_SHARED_DIR/bin/ && cp azcopy $AZ_BATCH_NODE_SHARED_DIR/bin/"  
```
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