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| Code Block |
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| language | bash |
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| title | Click here for the solution |
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| collapse | true |
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cds
mkdir BDIB_breseq
cp $BI/ngs_course/lambda_mixed_pop/data/* BDIB_breseq
cd BDIB_breseq
ls |
If the copy worked correctly you should see the following 2 files:
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| title | We have previously covered using scp to transfer files, but here we present another detailed example. Click to expand. |
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If you To use scp then you will need to run it in a terminal that is on your desktop and not on the remote TACC system. It can be tricky to figure out where the files are on the remote TACC system, because your desktop won't understand what $HOME, $WORK, $SCRATCH mean (they are only defined on TACC). To figure out the full path to your file, you can use the pwd command in your terminal on TACC in the window that you ran breseq in (it should contain an "output" folder). Rather than copying the entire contents of the folder which can be rather large, we are going to add a twist of compressing the entire folder into a single compressed archive using the tar command so that the size will be smaller and it will transfer faster: | Code Block |
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login1$ |
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| language | bash |
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| title | Command to type in TACC |
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| tar -czvf output.tar.gz output # the czvf options in order mean Create, Zip, Verbose, Force
pwd
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Then try a command like this on your desktop (if on a Linux machine or MacOS X): | Code Block |
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desktop1$ you can then copy paste that information (in the correct position) into the scp command on the desktop's command line: | Code Block |
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| language | bash |
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| title | Command to type in the desktop's terminal window |
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| scp -r username@lonestar<username>@lonestar.tacc.utexas.edu:<the_directory_returned_by_pwd>outputpwd>/output.tar.gz .
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It would be even better practice to archive and gzip the output directory before copying it using tar -cvzf to archive. Then copying that file and using tar -xvzf to unarchive it. |
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tar -xvzf output.tar.gz # the new "x" option at the front means eXtract |
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Navigate to the output directory in the finder and open the a file called index.html. Open this This will open the results in a web browser on your desktop and click around to take a look at the mutation predictions and summary informationwindow that you can click through different mutations and other information and see the evidence supporting it.
Example 2: E. coli data sets
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