> For the complete documentation index, see [llms.txt](https://jodyphelan.gitbook.io/tb-profiler/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://jodyphelan.gitbook.io/tb-profiler/quickstart/install.md).

# Install

TB-Profiler can be installed using a variety of different methods. The easiest is to use conda but you can also install manually.

### **Conda**

Conda can function as a package manages are is available [here](https://docs.conda.io/en/latest/miniconda.html). If you have conda make sure the bioconda and conda-forge channels are added:

```
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```

Then you can install with:

```
conda install -c bioconda tb-profiler
```

If this is taking a long time or complains about inconsistencies there are a few things we can do. The first is switching to `mamba` instal install. `mamba` basically is a drop-in replacement for conda, but is **a lot** faster. If you don't have it yet, you can install with:

```
conda install -c conda-forge mamba
```

Second, `tb-profiler` comes bundled with a lot of software. This often can cause compatibility issues with other software installed in your conda base environemnt. It is therefor recommended to intall `tb-profiler` in its own enviroment with:

```
mamba create -n tb-profiler tb-profiler
```

### **Manually**

It is possible to install manually. The following pre-requisites will be needed at runtime: *trimmomatic (>=v0.38), bwa (>=v0.7.17), minimap2 (>=v2.16), bowtie2 (>=v2.3.5), samtools (>=v1.9), bcftools (>=v1.9), GATK (>=v4.1.4.0), tqdm (>=v4.32.2) and parallel (>=v20190522)*. The pipeline should work and has been tested on the program versions indicated in parentheses.

To install the library, you can then use

```
pip3 install git+https://github.com/jodyphelan/TBProfiler.git
pip3 install git+https://github.com/jodyphelan/pathogen-profiler.git
mkdir `python -c "import sys; print(getattr(sys, 'base_prefix', getattr(sys, 'real_prefix', sys.prefix)));"`
tb-profiler update_tbdb
```

### Docker

The pipline can also be run through docker. This is handy when the above methods fail for whatever reason. Pull the latest image using:

```
docker pull quay.io/biocontainers/tb-profiler:4.3.0--pypyh5e36f6f_0
```

### Installation issues?

If the above method don't work please feel free to [raise an issue](https://github.com/jodyphelan/TBProfiler/issues). We'll try help you get up and running!


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://jodyphelan.gitbook.io/tb-profiler/quickstart/install.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.