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mkdir $WORK/src

Do one of the following, (or both if you want practice moving files around):

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1. Try to use 'wget -h' before clicking below. When using wget it is often helpful to right click on a link and select 'copy link address' when the file you want is available through a download link.

   Code Block
   language bash title How to use wget to download directly to TACC collapse true
   cd $WORK/src wget http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz

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1. Remember that scp has 2 parts after the command name just like the cp command: 1. the location the file currently is, and 2. the location you want to copy the file to. Most of the class has dealt with moving things from TACC to your computer, but in this case things will move the opposite direction, think about what needs to change about your SCP command to accomplish this.

   Code Block
   language bash title How to use SCP to transfer the downloaded file to TACC from your laptop (MAC) collapse true
   In a terminal window of your laptop not LS5 scp ~/Downloads/SPAdes-3.13.0-Linux.tar.gz <taccuserID>@ls5.tacc.utexas.edu:<$WORK pwd>/src # Note you need to replace $WORK with the output from the pwd command on TACC

Once the .tar.gz file has been placed in the $WORK/src folder using one of the above options, you need to extract the files.

cd $WORK
tar -xvzf SPAdes-3.13.0-Linux.tar.gz
# from the help file:
  # x = Extract
  # v = verbose
  # z = file is also gzipped
  # f = force 

Now that the files have been extracted you have a choice in how to use them: 1 option is to copy the binary files to a location that is already in your path (such as the $HOME/local/bin directory we set up for you in your .bashrc file), and the second option is to add the $WORK/src/SPAdes-3.13.0-Linux/bin folder to your path. This is a personal preference and I do not know how prevalent either choice is among researchers. I know that my preference is to copy executable to known locations in the path rather than add a ton of different directories to my path, but others may feel differently. Below I present both options:

Data

Tutorial assumes that you are on an idev node. If you are not sure please ask for help.

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