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Fix broken expansion boxes #346

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merged 4 commits into from
Nov 1, 2023
Merged

Fix broken expansion boxes #346

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6748ffc
Fix broken expansion boxes
bkmgit Jul 25, 2023
3b105a7
Use 'spoiler' rather than 'solution' for the platform-specific upload…
p-j-smith Oct 30, 2023
a5de280
Merge branch 'main' into patch-2
p-j-smith Oct 30, 2023
957ac35
Use contraction `you're` for consistency
p-j-smith Nov 1, 2023
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27 changes: 12 additions & 15 deletions episodes/05-writing-scripts.md
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Expand Up @@ -330,16 +330,12 @@ using a transfer program, it needs to be installed on your local machine, not yo

## Transferring Data Between your Local Machine and the Cloud

If you're using Windows with PuTTY instead of Git Bash, please select the alternative option here:
<select id="id_platform" name="platformlist" onchange="change_content_by_platform('id_platform');return false;">
If you are using Linux, Mac OS, or Windows with Git Bash on your local machine, you can use
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`scp` to upload data to your virtual machine.

<option value="unix" id="id_unix" selected> Linux, Mac OS, Git Bash </option>
<option value="win" id="id_win"> PuTTY </option>
</select>
::::::::::::::: spoiler

<div id="div_unix" style="display:block" markdown="1">

### Uploading Data to your Virtual Machine with scp
### SCP

`scp` stands for 'secure copy protocol', and is a widely used UNIX tool for moving files
between computers. The simplest way to use `scp` is to run it in your local terminal,
Expand Down Expand Up @@ -388,16 +384,19 @@ $ scp [email protected]:/home/dcuser/shell_data/untrimmed_fastq/scripted_bad_rea

Remember that in both instances, the command is run from your local machine, we've just flipped the order of the to and from parts of the command.
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we have


</div>
:::::::::::::::::::::::

If you are using Windows without Git Bash on your local machine, you can use `pscp.exe`
to upload data to your virtual machine.

<div id="div_win" style="display:block" markdown="1">
::::::::::::::: spoiler

### Uploading Data to your Virtual Machine with PSCP
### PCSP

If you're using a Windows PC without Git Bash, we recommend you use the *PSCP* program.
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you are

This program is from the same suite of tools as the PuTTY program we have been using to connect.

1. If you haven't done so, download pscp from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)
1. If you haven't done so, download *PSCP* from [http://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe](https://the.earth.li/~sgtatham/putty/latest/x86/pscp.exe)
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you have not

2. Make sure the *PSCP* program is somewhere you know on your computer. In this case,
your Downloads folder is appropriate.
3. Open the windows [PowerShell](https://en.wikipedia.org/wiki/Windows_PowerShell);
Expand Down Expand Up @@ -426,13 +425,11 @@ C:\User\your-pc-username\Downloads> pscp.exe [email protected]
C:\User\your-pc-username\Downloads
```

</div>
:::::::::::::::::::::::

:::::::::::::::::::::::::::::::::::::::: keypoints

- Scripts are a collection of commands executed together.
- Transferring information to and from virtual and local computers.

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