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1 | 1 | # Orientation |
2 | 2 |
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3 | 3 | The GitHub Codespaces environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. |
4 | | -However, you do need a (free) account to log in, and you should take a few minutes to familiarize yourself with the interface. |
| 4 | +However, you do need a (free) GitHub account to log in, and you should take a few minutes to familiarize yourself with the interface. |
5 | 5 |
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6 | | -If you have not yet done so, please follow [this link](../../envsetup/) before going any further. |
| 6 | +If you have not yet done so, please go through the [Environment Setup](../../envsetup/) mini-course before going any further. |
7 | 7 |
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8 | | -## Materials provided |
| 8 | +## Working directory |
| 9 | + |
| 10 | +Throughout this training course, we'll be working in the `hello-nextflow/` directory. |
| 11 | + |
| 12 | +Change directory now by running this command in the terminal: |
| 13 | + |
| 14 | +```bash |
| 15 | +cd hello-nextflow/ |
| 16 | +``` |
9 | 17 |
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10 | | -Throughout this training course, we'll be working in the `hello-nextflow/` directory, which loads by default when you open the training workspace. |
11 | | -This directory contains all the code files, test data and accessory files you will need. |
| 18 | +!!!tip |
| 19 | + |
| 20 | + If for whatever reason you move out of this directory, you can always use the full path to return to it, assuming you're running this within the Github Codespaces training environment: |
| 21 | + |
| 22 | + ```bash |
| 23 | + cd /workspaces/training/hello-nextflow |
| 24 | + ``` |
12 | 25 |
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13 | | -Feel free to explore the contents of this directory; the easiest way to do so is to use the file explorer on the left-hand side of the training workspace. |
| 26 | +Now let's have a look at the contents of this directory. |
| 27 | + |
| 28 | +## Materials provided |
| 29 | + |
| 30 | +You can explore the contents of this directory by using the file explorer on the left-hand side of the training workspace. |
14 | 31 | Alternatively, you can use the `tree` command. |
| 32 | + |
15 | 33 | Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity. |
16 | 34 |
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17 | 35 | Here we generate a table of contents to the second level down: |
@@ -60,12 +78,4 @@ If you run this inside `hello-nextflow`, you should see the following output: |
60 | 78 | The name and number in the filename correspond to the step of the relevant part of the course. |
61 | 79 | For example, the file `hello-world-4.nf` is the expected result of completing steps 1 through 4 of Part 1: Hello World. |
62 | 80 |
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63 | | -!!!tip |
64 | | - |
65 | | - If for whatever reason you move out of this directory, you can always run this command to return to it (within the training environment): |
66 | | - |
67 | | - ```bash |
68 | | - cd /workspaces/training/hello-nextflow |
69 | | - ``` |
70 | | - |
71 | | -Now, to begin the course, click on the arrow in the bottom right corner of this page. |
| 81 | +**Now, to begin the course, click on the arrow in the bottom right corner of this page.** |
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