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Conversion success! Unsure what Step2 entails #107

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grace-ac opened this issue Oct 27, 2017 · 14 comments
Closed

Conversion success! Unsure what Step2 entails #107

grace-ac opened this issue Oct 27, 2017 · 14 comments

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@grace-ac
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@grace-ac grace-ac commented Oct 27, 2017

Looks like it's working...?
capture

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@grace-ac grace-ac commented Oct 27, 2017

The .mzML are in Downloads!
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@grace-ac grace-ac commented Oct 27, 2017

I don't get what Step 2 is saying to do. What fasta files?

I'm experiencing general confusion.

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@grace-ac grace-ac changed the title Converting Raw to .mzML Conversion success! Unsure what Step2 entails Oct 27, 2017
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@grace-ac grace-ac commented Oct 27, 2017

May be easier to wait until we can speak with Jose.?

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@sr320 sr320 commented Oct 30, 2017

I will also edit protocol such that it makes more sense...

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@sr320 sr320 commented Nov 7, 2017

use this file (rename from .txt to .fa)
Cg_Giga_cont_prtc_AA.txt

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@grace-ac grace-ac commented Nov 7, 2017

I am on Step 2c and I am having some trouble with the awk thing.

This is what I have in a jupyter notebook so far:
capture

I'm wanting to see what the file looks like that was created by the Protein Digestion Simulator is Step 2b. Am I using the wrong thing?

The file is in the folder named "grace" on the desktop, so I am pretty positive I'm in the correct directory.

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@sr320 sr320 commented Nov 7, 2017

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@grace-ac grace-ac commented Nov 7, 2017

Ah ok, and no, I just installed anaconda - didn't know there were more things to install! I'm guessing that means "awk" won't work until things get installed, either.

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@sr320 sr320 commented Nov 7, 2017

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@kubu4 kubu4 commented Nov 7, 2017

Use Docker. ;)

I'll formulate real response shortly... (although, Docker is actually an easy solution).

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@kubu4 kubu4 commented Nov 7, 2017

Yes, the problem is because Bash is not installed on that computer (awk, head, tail, etc. are programs included with Bash).

Try following the instructions under the "Setup" section for Windows at this link: https://uwescience.github.io/2017-10-02-uw/

After installing, I'd recommend restarting the computer.

Then, fire up a Jupyter notebook and type the following in a cell and run the cell:

!which head

If things are working correctly, the output should be something like (i.e. a path to somewhere):

/usr/local/bin

Otherwise, you'll get the same error you got above. Please let me know how this plays out.

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@grace-ac grace-ac commented Nov 7, 2017

I followed the instructions and also went along with the video tutorial, but the same error came up:
capture

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@kubu4 kubu4 commented Nov 7, 2017

I think the actual issue here is the instructions in 2c are incomplete, right?

Step 2c needs explicit instructions on how to extract just the two columns needed.

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@sr320 sr320 commented Nov 7, 2017

Added instructions

@sr320 sr320 closed this Nov 7, 2017
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