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## Dependencies
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`CTDConverter` has the following python dependencies:
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- [CTDopts]
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- [CTDopts]
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- `lxml`
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- `pyyaml`
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- `ruamel.yaml`
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### Installing Dependencies
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We recommend the use of `conda` to manage all dependencies. If you're not sure what `conda` is, make sure to read the [using-conda](conda documentation).
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The easiest way to get you started with CTD conversion is to create a `conda` environment on which you'll install all dependencies. Using environments in `conda` allows you to have parallel, independent python environments, thus avoiding conflicts between libraries. If you haven't installed `conda`, check [conda-install](conda's installation guide).
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Once you've installed `conda`, create an environment named `ctd-converter` and list all dependencies, like so:
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15 |
Once you've installed `conda`, create an environment named `ctd-converter`, like so:
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```sh
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$ conda create --name ctd-converter --channel workflowconversion ctdopts lxml pyyaml libxml2=2.9.2
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$ conda create --name ctd-converter
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```
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[CTDopts] is a python module available on the `workflowconversion` channel in the Anaconda cloud. Of course, you could just download [CTDopts] and make it available through your `PYTHONPATH` environment variable, if you're into that. To get more information about how to install python modules, visit: https://docs.python.org/2/install/.
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`lxml` depends on `libxml2`. When you install `lxml` you'll get the latest version of `libxml2` (2.9.4) by default. You would usually want the latest version, but there is, however, a bug in validating XML files against a schema in this version of `libxml2`.
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If you require validation of input CTDs against a schema (which we recommend), you will need to downgrade to the latest known version of `libxml2` that works, namely, 2.9.2.
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You will now need to *activate* the environment by executing the following command:
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```sh
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$ source activate ctd-converter
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```
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Install the required dependencies as follows (the order of execution **is actually important**, due to transitive dependencies):
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```sh
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$ conda install --channel workflowconversion ctdopts
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$ conda install lxml
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32 |
$ conda install --channel conda-forge ruamel.yaml
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33 |
$ conda install libxml2=2.9.2
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34 |
```
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35 |
|
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36 |
`lxml` depends on `libxml2`. When you install `lxml` you'll get the latest version of `libxml2` (2.9.4) by default. You would usually want the latest version, but there is, however, a bug in validating XML files against a schema in this version of `libxml2`.
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37 |
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38 |
If you require validation of input CTDs against a schema (which we recommend), you will need to downgrade to the latest known version of `libxml2` that works, namely, 2.9.2.
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39 |
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40 |
You could just download dependencies manually and make them available through your `PYTHONPATH` environment variable, if you're into that. To get more information about how to install python modules without using `conda`, visit: https://docs.python.org/2/install/.
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## How to install `CTDConverter`
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`CTDConverter` is not a python module, rather, a series of scripts, so installing it is as easy as downloading the source code from https://github.com/genericworkflownodes/CTDConverter. Once you've installed all dependencies, downloaded `CTDConverter` and activated your `conda` environment, you're good to go.
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