### Install Nextflow

Source: https://github.com/seqeralabs/docs/blob/master/fusion_docs/get-started.md

Installs Nextflow on your system by downloading and executing the installation script. This is the primary method for new installations.

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

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

### Seqera Platform CLI Installation (Example)

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/cli/overview.md

This snippet demonstrates a typical installation command for the Seqera Platform CLI. It assumes a package manager or direct download method. Specific commands may vary based on the operating system and installation method.

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

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

### Seqera Platform CLI Installation (Example)

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/cli/overview.md

This snippet demonstrates a typical installation command for the Seqera Platform CLI. It assumes a package manager or direct download method. Specific commands may vary based on the operating system and installation method.

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

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

### Seqera Platform CLI Installation (Example)

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/cli/overview.md

This snippet demonstrates a typical installation command for the Seqera Platform CLI. It assumes a package manager or direct download method. Specific commands may vary based on the operating system and installation method.

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

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

### Seqera Platform CLI Installation (Example)

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.3/cli/overview.mdx

This snippet demonstrates a typical installation command for the Seqera Platform CLI. It assumes a package manager or direct download method. Specific commands may vary based on the operating system and installation method.

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

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

### Start and Check Platform Containers

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/enterprise/studios.md

Commands to start the Seqera Platform instance using Docker Compose and to verify that the platform containers are running.

```shell
docker compose -d up
docker ps
```

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

### Install Azcopy using Start Task

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/compute-envs/azure-batch.md

This shell command is used as a start task for an Azure Batch pool to install 'azcopy'. Azcopy is utilized for staging files onto and off of the compute nodes.

```Shell
echo "Installing azcopy"
cd /opt
curl -L https://aka.ms/downloadazcopy-v10-linux64 -o azcopy.tar.gz
tar -xzf azcopy.tar.gz
sudo mv azcopy/azcopy /usr/local/bin/
sudo setcap cap_net_raw+ep /usr/local/bin/azcopy
echo "azcopy installed"

```

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

### Install Azcopy using Start Task

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/compute-envs/azure-batch.md

This shell command is used as a start task for an Azure Batch pool to install 'azcopy'. Azcopy is utilized for staging files onto and off of the compute nodes.

```Shell
echo "Installing azcopy"
cd /opt
curl -L https://aka.ms/downloadazcopy-v10-linux64 -o azcopy.tar.gz
tar -xzf azcopy.tar.gz
sudo mv azcopy/azcopy /usr/local/bin/
sudo setcap cap_net_raw+ep /usr/local/bin/azcopy
echo "azcopy installed"

```

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

### Install Azcopy using Start Task

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/compute-envs/azure-batch.md

This shell command is used as a start task in Azure Batch to install the `azcopy` utility on each VM joining the pool. `azcopy` is essential for staging files to and from Azure Storage nodes.

```shell
echo "Installing azcopy..."
cd /tmp
wget -q https://aka.ms/downloadazcopy-v10-linux
chmod +x downloadazcopy-v10-linux
./downloadazcopy-v10-linux --install
echo "Azcopy installed."
```

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

### Start Platform Instance

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/enterprise/studios.md

Command to start the Seqera Platform instance in detached mode using Docker Compose.

```bash
docker compose -d up
```

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

### Update Nextflow

Source: https://github.com/seqeralabs/docs/blob/master/fusion_docs/get-started.md

Updates an existing Nextflow installation to the latest version. This command ensures you have the most recent features and bug fixes for Nextflow.

```bash
nextflow -self-update
```

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

### Nextflow Command-line Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx

Illustrates a typical Nextflow command invocation for running a pipeline, including version and profile specifications.

```bash
nextflow run <pipeline_name> -r <version> -profile <profile_name>
```

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

### Install Azcopy using Start Task

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/compute-envs/azure-batch.md

This shell command is used as a start task for an Azure Batch pool to install 'azcopy'. Azcopy is utilized for staging files onto and off of the compute nodes.

```Shell
echo "Installing azcopy"
cd /opt
curl -L https://aka.ms/downloadazcopy-v10-linux64 -o azcopy.tar.gz
tar -xzf azcopy.tar.gz
sudo mv azcopy/azcopy /usr/local/bin/
sudo setcap cap_net_raw+ep /usr/local/bin/azcopy
echo "azcopy installed"

```

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

### Get Seqerakit Help

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.3/seqerakit/installation.md

Shows the available commands and options for Seqerakit, providing a quick reference for its functionality. Use the `--help` or `-h` flag.

```Shell Session
seqerakit --help
```

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

### Install Azcopy using Start Task

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/compute-envs/azure-batch.md

This shell command is used as a start task in an Azure Batch pool to install Azcopy on the virtual machine. Azcopy is a command-line utility for copying files to and from Azure Blob Storage and Azure Files.

```shell
echo "Installing azcopy..."
cd /tmp
wget -q https://aka.ms/downloadazcopy-v10-linux
chmod +x downloadazcopy-v10-linux
./downloadazcopy-v10-linux --install-to=/usr/local/bin/
azcopy --version

```

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

### Install and Configure Seqera CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/cli/installation.md

Steps to download, make executable, and move the Seqera CLI to the system's PATH.

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

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

### Display Seqerakit Help Information

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/seqerakit/installation.md

Uses the '--help' or '-h' option to list all available commands and their options for Seqerakit.

```Bash
seqerakit --help
```

```Bash
seqerakit -h
```

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

### Get Seqerakit Version

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/seqerakit/installation.md

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

```bash
seqerakit --version
```

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

### Get Seqerakit Version

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/seqerakit/installation.md

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

```bash
seqerakit --version
```

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

### Get Seqerakit Version

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/seqerakit/installation.md

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

```bash
seqerakit --version
```

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

### Display Seqerakit Help Information

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/seqerakit/installation.md

Shows the available commands and options for Seqerakit using the --help or -h flag.

```Shell Session
seqerakit --help
```

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

### Get Seqerakit Version

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/seqerakit/installation.md

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

```bash
seqerakit --version
```

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

### Display Seqerakit Help Information

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/seqerakit/installation.md

Shows the available commands and options for Seqerakit using the --help or -h flag.

```Shell Session
seqerakit --help
```

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

### Display Seqerakit Help

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/seqerakit/installation.md

Displays the available commands and options for Seqerakit using the '--help' or '-h' flag. This provides an overview of Seqerakit's functionality.

```bash
seqerakit --help
```

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

### Example AWS SSM Get Parameter Response

Source: https://github.com/seqeralabs/docs/blob/master/fusion_docs/guide/snapshots.md

This is an example JSON response from the AWS CLI command to get the recommended ECS-optimized AMI parameter. It includes details like the image ID, ECS agent version, and runtime version.

```json
{
    "Parameter": {
        "Name": "/aws/service/ecs/optimized-ami/amazon-linux-2023/recommended",
        "Type": "String",
        "Value": "{\"ecs_agent_version\":\"1.88.0\",\"ecs_runtime_version\":\"Docker version 25.0.6\",\"image_id\":\"ami-0281c9a5cd9de63bd\",\"image_name\":\"al2023-ami-ecs-hvm-2023.0.20241115-kernel-6.1-x86_64\",\"image_version\":\"2023.0.20241115\",\"os\":\"Amazon Linux 2023\",\"schema_version\":1,\"source_image_name\":\"al2023-ami-minimal-2023.6.20241111.0-kernel-6.1-x86_64\"}",
        "Version": 61,
        "LastModifiedDate": "2024-11-18T17:08:46.926000+01:00",
        "ARN": "arn:aws:ssm:eu-central-1::parameter/aws/service/ecs/optimized-ami/amazon-linux-2023/recommended",
        "DataType": "text"
    }
}
```

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

### Display Seqerakit Help

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/seqerakit/installation.md

Displays the available commands and options for Seqerakit using the '--help' or '-h' flag. This provides an overview of Seqerakit's functionality.

```bash
seqerakit --help
```

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

### Install and Load R Packages for RNA-Seq

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/getting-started/rnaseq.mdx

Installs and loads essential R packages for RNA-Seq analysis, including limma, edgeR, ggplot2, and gplots. It ensures BiocManager is installed first.

```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 System Packages in R-IDE/VS Code/Xpra

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/studios/overview.md

Demonstrates how to install system-level packages using the `apt` package manager within a terminal window of R-IDE, Visual Studio Code, or Xpra environments.

```bash
apt install <packagename>
```

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

### Seqera Platform API Request Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-api-docs/docs/info/seqera-api.info.mdx

Demonstrates a POST request to the Seqera Platform API, including authorization and version headers, a URL with query parameters, and a request body.

```bash
curl -H "Authorization: Bearer QH..E5M=" \
     -H "Accept-Version:1" \
     -X POST https://api.cloud.seqera.io/domain/{item_id}?queryString={value} \
     -d { params: { "key":"value" } }
```

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

### Install Nextflow

Source: https://github.com/seqeralabs/docs/blob/master/fusion_docs/guide.md

Command to download and install Nextflow on your system. This script fetches the latest Nextflow release and makes it executable.

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

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

### Install and Load RNA-Seq Packages in R

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/getting-started/rnaseq.mdx

Installs and loads essential Bioconductor and CRAN packages for RNA-Seq analysis, including limma, edgeR, ggplot2, and gplots. Ensures BiocManager is installed first.

```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)
```

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

### Display Seqerakit Help

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/seqerakit/installation.md

Displays the available commands and options for Seqerakit using the '--help' or '-h' flag. This provides an overview of Seqerakit's functionality.

```bash
seqerakit --help
```

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

### Install and Configure Seqera CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/cli/installation.md

Steps to download, make executable, and move the Seqera CLI binary to the system's PATH. This ensures the CLI is accessible from any directory.

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

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

### Install and Load RNA-Seq Packages in R

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/getting-started/rnaseq.mdx

Installs and loads essential Bioconductor and CRAN packages for RNA-Seq analysis, including limma, edgeR, ggplot2, and gplots. Ensures BiocManager is installed first.

```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)
```

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

### Dockerfile with Python HTTP Server

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/data_studios/custom-envs.md

This Dockerfile example shows how to build a custom container environment that includes a Python HTTP server. It starts from a Seqera base image, installs Python, copies the `connect` binary, and configures the container to run a simple HTTP server listening on the port specified by the `CONNECT_TOOL_PORT` environment variable.

```docker
FROM public.cr.seqera.io/platform/connect-client:0.8 AS connect

FROM ubuntu:20.04
RUN apt-get update --yes && apt-get install --yes --no-install-recommends python3

COPY --from=connect /usr/bin/connect-client /usr/bin/connect-client
RUN /usr/bin/connect-client --install
ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]

CMD ["/usr/bin/bash", "-c", "python3 -m http.server $CONNECT_TOOL_PORT"]
```

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

### Install Seqera Platform CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/cli/overview.md

Instructions for installing the Seqera Platform CLI on different operating systems. This typically involves using a package manager or downloading a binary.

```shell
# Example installation command (specific command may vary based on OS and installation method)
# curl -s https://get.seqera.io/cli/install.sh | bash
```

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

### Install System Packages in Xpra

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/studios/overview.md

Instructions for installing system-level packages in a running Xpra session. This is done through a terminal window using the `apt install` command.

```Bash
apt install <package_name>
```

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

### Install and Load R Packages for RNA-Seq

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md

Installs and loads essential R packages like limma, edgeR, ggplot2, and gplots, which are necessary for performing RNA-Seq analysis and visualization. It ensures BiocManager is installed first.

```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 and Load R Packages for RNA-Seq

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/getting-started/rnaseq.mdx

Installs and loads essential R packages like limma, edgeR, ggplot2, and gplots, which are necessary for performing RNA-Seq analysis and visualization. It ensures BiocManager is installed first.

```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 Seqera Platform CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/cli/overview.mdx

Instructions for installing the Seqera Platform CLI on different operating systems. This typically involves using a package manager or downloading a binary.

```shell
# Example installation command (specific command may vary based on OS and installation method)
# curl -s https://get.seqera.io/cli/install.sh | bash
```

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

### Install and Load R Packages for RNA-Seq

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/getting-started/rnaseq.md

Installs and loads essential R packages like limma, edgeR, ggplot2, and gplots, which are necessary for performing RNA-Seq analysis and visualization. It ensures BiocManager is installed first.

```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)
```

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

### Display Seqerakit Help

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/seqerakit/installation.md

Displays the available commands and options for Seqerakit using the '--help' or '-h' flag. This provides an overview of Seqerakit's functionality.

```bash
seqerakit --help
```

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

### Nextflow Command-line Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/getting-started/quickstart-demo/view-run-information.md

Displays an example of a Nextflow command invocation used to run a pipeline, including version and profile flags.

```bash
nextflow run <pipeline> -r <version> -profile <profile>
```

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

### Get Seqerakit Version

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.3/seqerakit/installation.md

Displays the current version of the installed Seqerakit package. This can be done using either the `--version` or `-v` flag.

```Shell Session
seqerakit --version
```

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

### Nextflow Input Parameter Example (YAML)

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/getting-started/rnaseq.md

Example of how pipeline input parameters, such as the samplesheet location, can be specified in a YAML file for Nextflow execution.

```yaml
input: s3://my-bucket/samplesheet.csv
outdir: s3://my-bucket/results/
```

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

### Install and Configure Seqera CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/cli/installation.mdx

Steps to download, make executable, and move the Seqera CLI binary to the system's PATH. This ensures the CLI is accessible from any directory.

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

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

### Nextflow Input Parameter Example (JSON)

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_docs/getting-started/rnaseq.md

Example of how pipeline input parameters, such as the samplesheet location, can be specified in a JSON file for Nextflow execution.

```json
{
  "input": "s3://my-bucket/samplesheet.csv",
  "outdir": "s3://my-bucket/results/"
}
```

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

### Install Seqera Platform CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/cli/overview.mdx

Instructions for installing the Seqera Platform CLI on different operating systems. This typically involves using a package manager or downloading a binary.

```shell
# Example installation command (specific command may vary based on OS and installation method)
# curl -s https://get.seqera.io/cli/install.sh | bash
```

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

### Docker Infrastructure Recommendations

Source: https://github.com/seqeralabs/docs/blob/master/platform-cloud/docs/getting-started/production-checklist.md

Outlines infrastructure recommendations for deploying Seqera Platform using Docker Compose. It specifies instance sizes for the application, database, and Redis cache. It highlights that these are starting points and actual needs depend on pipeline and concurrency. Links to Docker resource constraint documentation are included.

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

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

### Install and Configure Seqera CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.2/cli/installation.mdx

Steps to download, make executable, and move the Seqera CLI binary to the system's PATH. This ensures the CLI is accessible from any directory.

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

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

### Dockerfile with Python HTTP server for Data Studios

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/data_studios/custom-envs.md

An example Dockerfile that builds a custom container environment for Data Studios, including a Python HTTP server. It starts from a Seqera base image, installs Python, copies the 'connect' binary, and configures the entry point, with the CMD setting up the HTTP server to listen on the dynamically provided port.

```docker
FROM public.cr.seqera.io/platform/connect-client:0.7 AS connect

FROM ubuntu:20.04
RUN apt-get update --yes && apt-get install --yes --no-install-recommends python3

COPY --from=connect /usr/bin/connect-client /usr/bin/connect-client
RUN /usr/bin/connect-client --install
ENTRYPOINT ["/usr/bin/connect-client", "--entrypoint"]

CMD ["/usr/bin/bash", "-c", "python3 -m http.server $CONNECT_TOOL_PORT"]
```

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

### Check Seqerakit Installation and Connection

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/seqerakit/installation.md

Runs the '--info' command to verify that Seqerakit is installed correctly and can connect to Seqera.

```Bash
seqerakit --info
```

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

### Azure Blob Container Path Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/compute-envs/azure-batch.md

Example of how to specify an Azure blob container as the pipeline work directory. This path is used by Nextflow for caching.

```bash
az://towerrgstorage-container/work
```

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

### Launch Pipeline with Seqera Platform CLI

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.1/cli/overview.md

Demonstrates how to launch a pipeline using the Seqera Platform CLI, similar to Nextflow, leveraging Platform's benefits for monitoring and resource management.

```bash
# Example command to launch a pipeline
# tw pipeline launch --name my-pipeline --repository https://github.com/user/my-pipeline.git
```

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

### Check Seqerakit Installation and Connection

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-24.1/seqerakit/installation.md

Runs the 'seqerakit --info' command to verify the installation, Platform CLI configuration, and connection to Seqera.

```Shell Session
seqerakit --info
```

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

### Tower Agent Configuration Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-22.4/_todo.md

This example demonstrates how to configure the Tower Agent, including handling non-standard home directory patterns with all-caps usernames and setting environment variables for optimal operation.

```Shell
# Example of launching tw-agent with specific user
USER=DCR tw-agent ...

# Example of setting work directory variable
export TOWER_AGENT_WORKDIR=/path/to/workdir
```

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

### nf-core/rnaseq Samplesheet Example

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-25.2/getting-started/rnaseq.md

An example of a samplesheet format required by the nf-core/rnaseq pipeline. It includes columns for sample name, FASTQ file paths (for paired-end reads), and strandedness information.

```text
sample | fastq_1 | fastq_2 | strandedness
GM12878_REP1 | s3://ngi-igenomes/test-data/rnaseq/SRX1603629_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX1603629_T1_2.fastq.gz | reverse
GM12878_REP2 | s3://ngi-igenomes/test-data/rnaseq/SRX1603630_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX1603630_T1_2.fastq.gz | reverse
K562_REP1 | s3://ngi-igenomes/test-data/rnaseq/SRX1603392_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX1603392_T1_2.fastq.gz | reverse
K562_REP2 | s3://ngi-igenomes/test-data/rnaseq/SRX1603393_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX1603393_T1_2.fastq.gz | reverse
MCF7_REP1 | s3://ngi-igenomes/test-data/rnaseq/SRX2370490_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX2370490_T1_2.fastq.gz | reverse
MCF7_REP2 | s3://ngi-igenomes/test-data/rnaseq/SRX2370491_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX2370491_T1_2.fastq.gz | reverse
H1_REP1 | s3://ngi-igenomes/test-data/rnaseq/SRX2370468_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX2370468_T1_2.fastq.gz | reverse
H1_REP2 | s3://ngi-igenomes/test-data/rnaseq/SRX2370469_T1_1.fastq.gz | s3://ngi-igenomes/test-data/rnaseq/SRX2370469_T1_2.fastq.gz | reverse
```

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

### Check Seqerakit Installation and Connection

Source: https://github.com/seqeralabs/docs/blob/master/platform-enterprise_versioned_docs/version-23.4/seqerakit/installation.md

Runs the 'seqerakit --info' command to verify the installation, Platform CLI configuration, and connection to Seqera.

```Shell Session
seqerakit --info
```