Feedback after reading tutorials #51
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…rial2 can use its output
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| ```bash | ||
| mkdir janis-tutorials | ||
| cd janis-tutorials |
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Creating janis-tutorials in tutorial 0. Assuming users will follow the tutorials in order (added a note to each about it, if not already there).
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| # If WGET is installed | ||
| wget -q -O- "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -xz | ||
| wget -q -O- "https://github.com/PMCC-BioinformaticsCore/janis-workshops/raw/master/janis-data.tar" | tar -x |
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I think the z needs to be there only if the file is gzipped. Removing it the command succeeded, although with warnings (will create an issue about the warnings).
| @@ -272,33 +274,30 @@ janis translate tools/alignment.py wdl | |||
| We'll run the workflow against the current directory. | |||
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| ```bash | |||
| janis run -o . --engine cwltool \ | |||
| janis run -o tutorial1 --engine cwltool \ | |||
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I think the intention is to keep tutorial 1 files within the tutorial1 directory. The alternative command in this tutorial creates tutorial1-run-with-cromwell, so after this change we will have both tutorial1-run-with-cromwell and tutorial1.
| @@ -280,13 +280,13 @@ Jobs: | |||
| [✓] samtoolsflagstat (N/A) | |||
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| Outputs: | |||
| - stats: $HOME/janis-tutorials/tutorial2/stats.txt | |||
| - stats: $HOME/janis-tutorials/tutorial2/stats | |||
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There was no stats.txt for me, only stats? Not sure if it was supposed to be .txt, maybe a different version of the tool used, or maybe I missed a step somewhere?
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| modules = ["janis_assistant." + p for p in sorted(find_packages("./janis_assistant"))] | |||
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| fixed_unix_version = f"janis-pipelines.unix==" + JANIS_UNIX_VERSION | |||
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Already defined up in the same code block with the same value ☝️
Hello,
I learned about Janis yesterday after an e-mail sent to the AU/NZ RSE mailing list. Really interesting project, and the code is super organized, and the docs are beyond great! 👏
The tutorials appeared to be super easy to follow, and I was really impressed when the first workflow ran without errors, and quite fast too.
This pull request includes typos, re-wording, and a couple places where the directory or command was incorrect (I will add notes to this PR).
The main change, I think, is the last commit. When I was in tutorial 1, I realized my
~/janisdirectory now had a mix of files that I could maintain, but most of them would have to be nuked if I wanted to keep it organized. However, tutorial 1 usedjanis-tutorialsfolder, keeping the newly created files isolated from the rest in~/janis.So the last commit is me trying to move all the tutorial data under
~/janis/janis-tutorials. It is similar to what you have with Cylc tutorials, or Airflow tutorials I think. Users may keep the tutorial files, or simply discard them by deleting~/janis/janis-tutorials.If this change is not really OK, I'd be happy to remove that part 👍
Also, I found a couple places where the output or the text in the tutorial did not match with what I had in my computer, but I will look at existing issues and create new ones later if necessary.
Thanks again!
Bruno