# Use custom channels

By default, conda-exec searches `conda-forge` for packages. You can specify
alternative or additional channels from the CLI or inside script metadata.

## Specify a channel from the CLI

Use `-c` or `--channel` to search a different channel:

```bash
conda exec -c bioconda samtools view input.bam
```

## Use multiple channels

Repeat `-c` to add multiple channels. They are searched in the order given:

```bash
conda exec -c bioconda -c defaults samtools view input.bam
```

```{important}
When you pass `-c`, the default `conda-forge` channel is not added
automatically. If your packages depend on `conda-forge`, you must include
it explicitly.
```

Include `conda-forge` alongside other channels when needed:

```bash
conda exec -c conda-forge -c bioconda samtools view input.bam
```

## Bioinformatics example

Many bioinformatics tools live in the `bioconda` channel and depend on
packages from `conda-forge`. Specify both:

```bash
conda exec -c conda-forge -c bioconda minimap2 -a ref.fa reads.fq > out.sam
```

## Declare channels in script metadata

For Python scripts with [PEP 723](https://peps.python.org/pep-0723/)
inline metadata, declare channels in the `[tool.conda]` table:

```python
# /// script
# [tool.conda]
# channels = ["conda-forge", "bioconda"]
# dependencies = ["samtools>=1.19", "pysam"]
# ///

import pysam
print(pysam.__version__)
```

```bash
conda exec script.py
```

## Combine script channels with CLI channels

```{tip}
Channels are searched in order. Channels declared in script metadata come
first, followed by any CLI channels. Put your preferred channel first to
give it higher priority.
```

CLI channels (`-c`) are appended after channels declared in script metadata.
Given a script that declares `channels = ["conda-forge"]`, running:

```bash
conda exec -c bioconda script.py
```

resolves packages using `["conda-forge", "bioconda"]` in that order.

If neither the script metadata nor the CLI provides channels, `conda-forge`
is used as the default.

## How channels affect caching

Different channel combinations produce different cache keys. Running the
same tool with different `-c` flags creates separate cached environments:

```bash
conda exec ruff check .                 # cached as ruff--<hash1>
conda exec -c defaults ruff check .     # cached as ruff--<hash2>
```