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Conda edits for JOSE paper #475

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Nov 18, 2021
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Conda edits for JOSE paper #475

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clarify vidlet topics, add export option
marisalim Nov 15, 2021
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add note about binder (base)
marisalim Nov 15, 2021
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28 changes: 19 additions & 9 deletions docs/General-Tools/Introduction-to-Conda/conda2.md
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Expand Up @@ -2,7 +2,7 @@

Let's get started with conda!

To follow along with this lesson, we are using a [binder](https://binder.pangeo.io/) with an Rstudio interface. Binders use collections of files from Github repositories with instructions on software installation to create small (and free!) computing environments. They are used for teaching and demonstrating software functionality or analysis workflows.
To follow along with this lesson, we have included several short video demonstrations of the steps described in this tutorial. We are using a [binder](https://binder.pangeo.io/) with an Rstudio interface. Binders use collections of files from Github repositories with instructions on software installation to create small (and free!) computing environments. They are used for teaching and demonstrating software functionality or analysis workflows.

Open the binder for this lesson in a **new tab** (i.e., by typing ++ctrl++ and clicking link): [Click me to launch binder!](https://binder.pangeo.io/v2/gh/nih-cfde/training-rstudio-binder/conda-workshop-march2021?urlpath=rstudio){:target="_blank"}

Expand All @@ -12,7 +12,7 @@ It may take 3-4 minutes for the binder to load!

For this lesson, we are using Rstudio to teach you conda because it consolidates showing the conda commands, terminal, and file system all on 1 screen. In practice, you can use conda through a command-line terminal interface without Rstudio.

We are using 3 of the Rstudio panels for this lesson: Source panel to run conda commands, Terminal panel to execute code, and File panel to view input/output files. You can rearrange the panels to help with viewing:
We are using 3 of the Rstudio panels for this lesson: Source panel to run conda commands, Terminal panel to execute code, and File panel to view input/output files. You can rearrange and minimize unused panels to help with viewing, as shown in the video below:

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_id1ezdq9&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_tndww4gg" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Expand All @@ -36,8 +36,6 @@ The conda installer sets up two things: Conda and the base environment (also cal

Image credit: [Gergely Szerovay](https://www.freecodecamp.org/news/why-you-need-python-environments-and-how-to-manage-them-with-conda-85f155f4353c/)

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_yzxi4s59&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_ucohpz4x" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Setup the conda installer and initialize the settings:

```
Expand All @@ -49,13 +47,15 @@ The binder auto-generates a very long command prompt. We will shorten it to `$`:
echo "PS1='\w $ '" >> .bashrc
```

Re-start terminal for the changes to take effect (type `exit` and then open a new terminal).
Re-start terminal for the changes to take effect (type `exit` and then open a new terminal). These steps are demonstrated in the video below:

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_yzxi4s59&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_ucohpz4x" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

We are currently in the `(base)` conda environment.
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### Conda channels: Searching for software

The channels are places where conda looks for packages. The default channel after conda installation is set to Anaconda Inc's channels (Conda's Developer).
The channels are places where conda looks for software packages. The default channel after conda installation is set to Anaconda Inc's channels (Conda's Developer). Below, we demonstrate how to list the binder's default channels and the `(base)` environment packages, after which we add new channels and set channel priority:

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_j2mmgrkh&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_5max8sqt" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Expand Down Expand Up @@ -172,7 +172,7 @@ Search for software (fastqc):
fastqc 0.11.9 0 bioconda
```

Now, let's create a conda environment with fastqc installed in it.
Now, let's create a conda environment with fastqc installed in it, as demonstrated below:

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_d3lxef1n&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_zf41375u" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Expand Down Expand Up @@ -271,7 +271,7 @@ echo $PATH
The following methods use an external file to specify the packages to install:

#### Method 3: specify software to install with a YAML file
Often, it's easier to create environments and install software using a YAML file that specifies all the software to be installed. For our example, we are using a file called `test.yml`.
Often, it's easier to create environments and install software using a YAML file that specifies all the software to be installed as demonstrated in the video. For our example, we are using a file called `test.yml`.

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_stc3zu6d&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_6n7tlxwg" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Expand Down Expand Up @@ -312,6 +312,16 @@ conda activate qc_yaml
conda list
```

!!! info

Note that you can export conda environments as YAML files as well. The [`--from-history` option](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#exporting-an-environment-file-across-platforms) outputs only the packages you've installed in this environment, as opposed to all the other default packages in the environment.

```
conda activate qc_yaml
conda env export --from-history > qc_env.yml
conda deactivate
```

#### Method 4: Install exact environment

For this approach, we export a list of the exact software package versions installed in a given environment and use it to set up new environments. This set up method won't necessarily install the latest version of a given program, but it will replicate the exact environment set up you exported from.
Expand Down Expand Up @@ -361,7 +371,7 @@ For this reason, and in practice, people often manage software for their workflo

### Running FastQC in a conda environment

Let's run a small analysis with FastQC in the `fqc` environment we created above.
Let's run a small analysis with FastQC in the `fqc` environment we created above:

<iframe id="kaltura_player" src="https://cdnapisec.kaltura.com/p/1770401/sp/177040100/embedIframeJs/uiconf_id/29032722/partner_id/1770401?iframeembed=true&playerId=kaltura_player&entry_id=1_v9ijwu6g&flashvars[mediaProtocol]=rtmp&amp;flashvars[streamerType]=rtmp&amp;flashvars[streamerUrl]=rtmp://www.kaltura.com:1935&amp;flashvars[rtmpFlavors]=1&amp;flashvars[localizationCode]=en&amp;flashvars[leadWithHTML5]=true&amp;flashvars[sideBarContainer.plugin]=true&amp;flashvars[sideBarContainer.position]=left&amp;flashvars[sideBarContainer.clickToClose]=true&amp;flashvars[chapters.plugin]=true&amp;flashvars[chapters.layout]=vertical&amp;flashvars[chapters.thumbnailRotator]=false&amp;flashvars[streamSelector.plugin]=true&amp;flashvars[EmbedPlayer.SpinnerTarget]=videoHolder&amp;flashvars[dualScreen.plugin]=true&amp;flashvars[Kaltura.addCrossoriginToIframe]=true&amp;&wid=1_672rs9xp" width="608" height="402" allowfullscreen webkitallowfullscreen mozAllowFullScreen allow="autoplay *; fullscreen *; encrypted-media *" sandbox="allow-forms allow-same-origin allow-scripts allow-top-navigation allow-pointer-lock allow-popups allow-modals allow-orientation-lock allow-popups-to-escape-sandbox allow-presentation allow-top-navigation-by-user-activation" frameborder="0" title="Kaltura Player"></iframe>

Expand Down