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Installation instructions for MacOS #1

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@ -9,8 +9,54 @@ https://github.com/psychoinformatics-de/processing-workflow.
adswa commented 2021-08-03 06:57:01 +00:00 (Migrated from github.com)
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- [DataLad](http://www.datalad.org): Please make sure that you have installed a recent version of DataLad (`0.14.3` or higher), as well as recent versions of its dependencies (git, `2.24.0` or higher; git-annex, `8.20*` or higher). Installation instructions are available at: [http://handbook.datalad.org](http://handbook.datalad.org/en/latest/intro/installation.html#install).

I would probably cut this - it is true for some systems, but I wouldn't want to force e.g. a pip user to get a separate conda environment, or a Windows user to fight with two separate Python installations.

```suggestion - [DataLad](http://www.datalad.org): Please make sure that you have installed a recent version of DataLad (`0.14.3` or higher), as well as recent versions of its dependencies (git, `2.24.0` or higher; git-annex, `8.20*` or higher). Installation instructions are available at: [http://handbook.datalad.org](http://handbook.datalad.org/en/latest/intro/installation.html#install). ``` I would probably cut this - it is true for some systems, but I wouldn't want to force e.g. a ``pip`` user to get a separate ``conda`` environment, or a Windows user to fight with two separate Python installations.
adswa commented 2021-08-03 07:02:11 +00:00 (Migrated from github.com)
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I would probably phrase this a bit less like "your OS is not supported" and rather like "here is how you do it". Below is a potential suggestion:

An installation of [Singularity on MacOS(https://sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac) requires using a virtual machine. It is recommended to use [VirtualBox](https://www.virtualbox.org) and (optionally) [Vagrant](https://www.vagrantup.com) software. This software can be installed via [Homebrew](https://brew.sh) package manager.
I would probably phrase this a bit less like "your OS is not supported" and rather like "here is how you do it". Below is a potential suggestion: ```suggestion An installation of [Singularity on MacOS(https://sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac) requires using a virtual machine. It is recommended to use [VirtualBox](https://www.virtualbox.org) and (optionally) [Vagrant](https://www.vagrantup.com) software. This software can be installed via [Homebrew](https://brew.sh) package manager. ```
adswa commented 2021-08-03 07:05:12 +00:00 (Migrated from github.com)
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Naive question: Do I need to do this before or after starting the VM?

Naive question: Do I need to do this before or after starting the VM?
adswa commented 2021-08-03 07:07:51 +00:00 (Migrated from github.com)
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Maybe this paragraph can move upwards, or become a footnote of the section

Please substitute the value of the $VM variable with a name of your Vagrant box (debian/buster64 in this example
?

Maybe this paragraph can move upwards, or become a footnote of the section > Please substitute the value of the `$VM` variable with a name of your Vagrant box (`debian/buster64` in this example ?
adswa commented 2021-08-03 07:09:16 +00:00 (Migrated from github.com)
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Probably worthwhile to note something like

Lastly, install the required software, as described in the ["Software requirements for automatic recomputation"](#software-requirements-for-automatic-recomputation) section above in your VM, as if your operating system was Linux.
Probably worthwhile to note something like ```suggestion Lastly, install the required software, as described in the ["Software requirements for automatic recomputation"](#software-requirements-for-automatic-recomputation) section above in your VM, as if your operating system was Linux. ```
m-wierzba commented 2021-08-03 07:46:38 +00:00 (Migrated from github.com)
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Yes, I agree.

Yes, I agree.
m-wierzba commented 2021-08-03 07:47:44 +00:00 (Migrated from github.com)
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Sounds good. :)

Sounds good. :)
m-wierzba commented 2021-08-03 07:54:43 +00:00 (Migrated from github.com)
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It could become a footnote.

The intended meaning was: "If you wan't to spare yourself trouble of installing Singularity by yourself, this is the way to go."

It could become a footnote. The intended meaning was: "If you wan't to spare yourself trouble of installing Singularity by yourself, this is the way to go."
m-wierzba commented 2021-08-03 07:58:50 +00:00 (Migrated from github.com)
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Agree, I would only split it into smaller chunks like so:

Lastly, install the required software in your VM, as if your operating system was Linux. Please follow instructions described in the ["Software requirements for automatic recomputation"](#software-requirements-for-automatic-recomputation) section above.
Agree, I would only split it into smaller chunks like so: ```suggestion Lastly, install the required software in your VM, as if your operating system was Linux. Please follow instructions described in the ["Software requirements for automatic recomputation"](#software-requirements-for-automatic-recomputation) section above. ```
m-wierzba commented 2021-08-03 08:06:34 +00:00 (Migrated from github.com)
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I believe this needs to be done once the VM is initialised, so after:

$ export VM=debian/buster64 && \
    vagrant init $VM

There's a possibility that you need to take your VM down and up again for the configuration changes to be applied.

I believe this needs to be done once the VM is [initialised](https://www.vagrantup.com/docs/cli/init), so after: ``` $ export VM=debian/buster64 && \ vagrant init $VM ``` There's a possibility that you need to take your VM down and up again for the configuration changes to be applied.
adswa commented 2021-08-03 08:19:16 +00:00 (Migrated from github.com)
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The intended meaning was: "If you wan't to spare yourself trouble of installing Singularity by yourself, this is the way to go."

Makes sense! its probably just fair to link to this upfront, so that people that do want to spare themselves the trouble know about this right away.

> The intended meaning was: "If you wan't to spare yourself trouble of installing Singularity by yourself, this is the way to go." Makes sense! its probably just fair to link to this upfront, so that people that do want to spare themselves the trouble know about this right away.
adswa commented 2021-08-03 08:19:27 +00:00 (Migrated from github.com)
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cool, sounds great!

cool, sounds great!
adswa commented 2021-08-03 08:20:17 +00:00 (Migrated from github.com)
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ok, cool. Do you want to add this, or refer to the docs for it?

ok, cool. Do you want to add this, or refer to the docs for it?
## Software requirements for automatic recomputation
- [DataLad](http://www.datalad.org)
- [Singularity](https://sylabs.io/docs/)
Software requirements for the worflow are described in details [here](https://github.com/psychoinformatics-de/fairly-big-processing-workflow#software-requirements).
If you're not planning to use any job scheduling / batch processing system (e.g. [HTCondor](https://research.cs.wisc.edu/htcondor/), [SLURM](https://slurm.schedmd.com/documentation.html)), but would simply like to run the example below, make sure to have the following software installed:
- [DataLad](http://www.datalad.org): Please make sure that you have installed a recent version of DataLad (`0.14.3` or higher), as well as recent versions of its dependencies (git, `2.24.0` or higher; git-annex, `8.20*` or higher). Installation instructions are available at: [http://handbook.datalad.org](http://handbook.datalad.org/en/latest/intro/installation.html#install).
- [Singularity](https://sylabs.io/docs/): In principle, no specific version of Singularity is required. If you're not sure what version to use, simply install the most recent one. Installation instructions can be found [here](https://sylabs.io/docs/).
Make sure to have your [Git identity](http://handbook.datalad.org/en/latest/intro/installation.html#initial-configuration) set up.
## Installation tips for MacOS
An installation of [Singularity on MacOS](https://sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac) requires using a virtual machine. It is recommended to use [VirtualBox](https://www.virtualbox.org) and (optionally) [Vagrant](https://www.vagrantup.com) software. This software can be installed via [Homebrew](https://brew.sh) package manager.
```
$ brew install --cask virtualbox && \
brew install --cask vagrant && \
brew install --cask vagrant-manager
```
The easiest way to start is to browse the [public Vagrant box catalog](https://app.vagrantup.com/boxes/search) for a Vagrant box matching your use case. Here, a box can be undestood as a base image of an operating system environment.
First, create and enter a directory to be used with your virtual machine:
```
$ mkdir vm-tutorial && \
cd vm-tutorial
```
Next, initialise your virtual machine. Please substitute the value of the `$VM` variable with a name of your Vagrant box (`debian/buster64` in this example).
<ul><b>IMPORTANT NOTE:</b> The Singularity community maintains <a href="https://app.vagrantup.com/boxes/search?page=1&provider=&q=sylabs&sort=downloads&utf8=✓">a set of Vagrant boxes</a> too. These boxes have Singularity software already included and ready to use.</ul>
```
$ export VM=debian/buster64 && \
vagrant init $VM
```
Make sure to allocate enough memory for your virtual machine. This can be done by editing the `vb.memory` parameter in the corresponding Vagrantfile (Vagrant configuration file). This file is automatically created in you virtual machine's directory.
Next, issue the following commands to bring your virtual machine up:
```
$ vagrant up && \
vagrant ssh
```
Lastly, install the required software in your VM, as if your operating system was Linux. Please follow instructions described in the ["Software requirements for automatic recomputation"](#software-requirements-for-automatic-recomputation) section above.
## How to recompute