# Installing from source

## Essentials

If you don't have apt-get, Homebrew, or conda, here's the list of requirements and URLs with installation instructions:

* **Ruby**: <https://www.ruby-lang.org/>. Required: v2.1+, recommended: v2.3+.
* **Python**: <https://www.python.org/>.
* **R**: <http://www.r-project.org/>.
* **SQLite3**: <https://www.sqlite.org/>.
* **NCBI BLAST+**: ftp\://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST.
* **HMMer**: <http://hmmer.janelia.org/software>. Required: v3.0+.
* **Bedtools**: <http://bedtools.readthedocs.org/en/latest/>.
* **Prodigal**: <http://prodigal.ornl.gov>.
* **IDBA**: <http://i.cs.hku.hk/~alse/hkubrg/projects/idba>. Required flavor:

  IDBA-UD.
* **MCL**: <http://micans.org/mcl/>.
* **Barrnap**: <http://www.vicbioinformatics.com/software.barrnap.shtml>.
* **Scythe**: <https://github.com/vsbuffalo/scythe>. Required: v0.991+.
* **FastQC**: <http://www.bioinformatics.babraham.ac.uk/projects/fastqc>.
* **SolexaQA++**: <http://solexaqa.sourceforge.net>. Required: v3.1.3+.
* **FastANI** (optional): <https://github.com/ParBLiSS/FastANI>. Required: v1.1+.
* **Diamond** (optional): <http://ab.inf.uni-tuebingen.de/software/diamond>. Required: v0.9.20+.

Diamond is optional but strongly recommended. Indexing can be performed much faster with Diamond, searching of some databases depend on it, and it's required by the MyTaxa utils. FastANI is also recommended, since searching some databases depend on it.

## R packages

The full list of R packages is automatically installed by MiGA. However, we will install one package here to make sure everything is properly initialized.

```bash
Rscript -e "install.packages('ape', repos = 'http://cran.rstudio.com/')"
```

## MyTaxa utils

If you want to activate the [MyTaxa](https://github.com/bio-miga/miga/tree/0413f0c757dafd1c3f434abbb30b61514c2868d8/manual/part2/part5/workflow.md#mytaxa) and [MyTaxa Scan](https://github.com/bio-miga/miga/tree/0413f0c757dafd1c3f434abbb30b61514c2868d8/manual/part2/part5/workflow.md#mytaxa-scan) steps, follow the instructions to install the [MyTaxa Utils](/master/part2/requirements/mytaxa.md).


---

# Agent Instructions: 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://manual.microbial-genomes.org/master/part2/requirements/source.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.