Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ac document #195

Merged
merged 4 commits into from
Jan 1, 2025
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 8 additions & 2 deletions .github/workflows/cgatcore_python.yml
Original file line number Diff line number Diff line change
Expand Up @@ -81,9 +81,15 @@ jobs:

- name: Install MkDocs and Dependencies
run: |
pip install mkdocs mkdocs-material mkdocstrings[python]
pip install mkdocs \
mkdocs-material \
mkdocstrings[python] \
pymdown-extensions \
mkdocs-material[imaging]

- name: Build and Deploy MkDocs Site
run: mkdocs gh-deploy --force --clean
run: |
mkdocs build
mkdocs gh-deploy --force --clean
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
39 changes: 0 additions & 39 deletions docs/defining_workflow/run_parameter.md

This file was deleted.

26 changes: 13 additions & 13 deletions docs/getting_started/examples.md
Original file line number Diff line number Diff line change
Expand Up @@ -228,13 +228,13 @@ When running the pipeline, make sure to specify `--no-cluster` as a command line
- **Logs**: Check the log files generated during the pipeline run for detailed error messages.
- **Support**: For further assistance, refer to the [CGAT-core documentation](https://cgat-developers.github.io/cgat-core/) or raise an issue on our [GitHub repository](https://github.com/cgat-developers/cgat-core/issues).

## CGAT-core Examples
## CGAT-core Examples {#cgat-core-examples}

This guide provides practical examples of CGAT-core pipelines for various use cases, from basic file processing to complex genomics workflows.

## Quick Start Examples
## Quick Start Examples {#quick-start-examples}

### Hello World Pipeline
### Hello World Pipeline {#hello-world-pipeline}

```python
"""hello_world.py - Simple CGAT pipeline example
Expand Down Expand Up @@ -271,7 +271,7 @@ if __name__ == "__main__":
sys.exit(P.main(sys.argv))
```

### Configuration Example
### Configuration Example {#configuration-example}

```yaml
# pipeline.yml
Expand All @@ -287,9 +287,9 @@ cluster:
memory_default: 1G
```

## Real-World Examples
## Real-World Examples {#real-world-examples}

### 1. Genomics Pipeline
### 1. Genomics Pipeline {#genomics-pipeline}

This example demonstrates a typical RNA-seq analysis pipeline:

Expand Down Expand Up @@ -380,7 +380,7 @@ if __name__ == "__main__":
sys.exit(P.main(sys.argv))
```

### 2. Data Processing Pipeline
### 2. Data Processing Pipeline {#data-processing-pipeline}

Example of a data processing pipeline with S3 integration:

Expand Down Expand Up @@ -455,7 +455,7 @@ if __name__ == "__main__":
sys.exit(P.main(sys.argv))
```

### 3. Image Processing Pipeline
### 3. Image Processing Pipeline {#image-processing-pipeline}

Example of an image processing pipeline:

Expand Down Expand Up @@ -522,9 +522,9 @@ if __name__ == "__main__":
sys.exit(P.main(sys.argv))
```

## Best Practices
## Best Practices {#best-practices}

### 1. Resource Management
### 1. Resource Management {#resource-management}

```python
@transform("*.bam", suffix(".bam"), ".sorted.bam")
Expand All @@ -550,7 +550,7 @@ def sort_bam(infile, outfile):
P.run(statement)
```

### 2. Error Handling
### 2. Error Handling {#error-handling}

```python
@transform("*.txt", suffix(".txt"), ".processed")
Expand All @@ -571,7 +571,7 @@ def robust_processing(infile, outfile):
P.cleanup_tmpdir()
```

### 3. Configuration Management
### 3. Configuration Management {#configuration-management}

```yaml
# pipeline.yml - Example configuration
Expand Down Expand Up @@ -611,7 +611,7 @@ s3:
max_concurrency: 10
```

## Running the Examples
## Running the Examples {#running-the-examples}

1. **Setup Configuration**
```bash
Expand Down
18 changes: 9 additions & 9 deletions docs/getting_started/installation.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

The following sections describe how to install the `cgatcore` framework.

## Conda installation
## Conda installation {#conda-installation}

The preferred method of installation is using Conda. If you do not have Conda installed, you can install it using [Miniconda](https://conda.io/miniconda.html) or [Anaconda](https://www.anaconda.com/download/#macos).

Expand All @@ -12,21 +12,21 @@ The preferred method of installation is using Conda. If you do not have Conda in
conda install -c conda-forge -c bioconda cgatcore
```

### Prerequisites
### Prerequisites {#prerequisites}

Before installing `cgatcore`, ensure that you have the following prerequisites:

- **Operating System**: Linux or macOS
- **Python**: Version 3.6 or higher
- **Conda**: Recommended for dependency management

### Troubleshooting
### Troubleshooting {#troubleshooting}

- **Conda Issues**: If you encounter issues with Conda, ensure that the Bioconda and Conda-Forge channels are added and prioritized correctly.
- **Pip Dependencies**: When using pip, manually install any missing dependencies listed in the error messages.
- **Script Errors**: If the installation script fails, check the script's output for error messages and ensure all prerequisites are met.

### Verification
### Verification {#verification}

After installation, verify the installation by running:

Expand All @@ -41,15 +41,15 @@ print(cgatcore.__version__)

This should display the installed version of `cgatcore`.

## Pip installation
## Pip installation {#pip-installation}

We recommend installation through Conda because it manages dependencies automatically. However, `cgatcore` is generally lightweight and can also be installed using the `pip` package manager. Note that you may need to manually install other dependencies as needed:

```bash
pip install cgatcore
```

## Automated installation
## Automated installation {#automated-installation}

The preferred method to install `cgatcore` is using Conda. However, we have also created a Bash installation script, which uses [Conda](https://conda.io/docs/) under the hood.

Expand Down Expand Up @@ -78,7 +78,7 @@ conda activate cgat-c

The installation script will place everything under the specified location. The aim of the script is to provide a portable installation that does not interfere with existing software environments. As a result, you will have a dedicated Conda environment that can be activated as needed to work with `cgatcore`.

## Manual installation
## Manual installation {#manual-installation}

To obtain the latest code, check it out from the public Git repository and activate it:

Expand All @@ -94,7 +94,7 @@ To update to the latest version, simply pull the latest changes:
git pull
```

## Installing additional software
## Installing additional software {#installing-additional-software}

When building your own workflows, we recommend using Conda to install software into your environment where possible. This ensures compatibility and ease of installation.

Expand All @@ -105,7 +105,7 @@ conda search <package>
conda install <package>
```

## Accessing the libdrmaa shared library
## Accessing the libdrmaa shared library {#accessing-libdrmaa}

You may also need access to the `libdrmaa.so.1.0` C library, which can often be installed as part of the `libdrmaa-dev` package on most Unix systems. Once installed, you may need to specify the location of the DRMAA library if it is not in a default library path. Set the `DRMAA_LIBRARY_PATH` environment variable to point to the library location.

Expand Down
Loading
Loading