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Code Block
languagebash
titleThe following command is then used to install miniconda
bash Miniconda3-latest-Linux-x86_64.sh
logout
#log back in using the ssh command. 
conda config --set auto_activate_base false

Following the installation prompts you will need to:

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Code Block
languagebash
titleas per the directions at the end of the installation process, logout, log back in, and disable conda base environment being activated
logout
#log back in using the ssh command. 
conda config --set auto_activate_base false
conda config --set channel_priority strict

For help with the ssh command please refer back to Windows10 or MacOS tutorials. If you log out and back in 1 more time, what do you notice is different?

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channels: - conda-forge - bioconda - defaults channel_priority: strict

There will be a post class tutorial of how to add channels permanently if you feel this is something you would benefit from after the class.

Tip
titleConda Channels

By the end of this course you may find that the 'bioconda' channel is full of lots of programs you want to use, and may choose to permanently add it to your list of channels so the above command conda install fastqc and others used in this course would work without having to go through the intermediate of searching for the specific installation commands, or finding what channel the program you want is in. Information about how to do this, as well as more detailed information of why it is bad practice to go around adding large numbers of channels can be found here. Similarly, when we get to the read mapping tutorial, we will go over the conda-forge channel which is also very helpful to have.

No Format
titlesuggested contents of .condarc file

For now, use the error message you saw above to try to install the fastqc program yourself.

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In previous years, the pip installation program was used to install a few programs. While those programs will be installed through conda this year, the link here is provided to give a detailed walk through of how to use pip on TACC resources. This is particularly helpful for making use of the '--user' flag during the installation process as you do not have the expected permissions to install things in the default directories.

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