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sstadick / perbase

Per-base per-nucleotide depth analysis
MIT License
115 stars 13 forks source link

ubuntu cant find perbase #56

Closed JMNGLS closed 1 year ago

JMNGLS commented 1 year ago

Sorry i am a new bioinformatician trying to train myself. It looks like perbase can do exactly what i need, but i am having trouble installing it! Seeing the error code: E: Unable to locate package perbase

I don't see perbase on packages.ubuntu.com I am excited about using perbase, any help or hints about how to get the program would be appreciated.

sstadick commented 1 year ago

Hi! Thanks for making an issue! Checkout the "Installation" section of the readme for instructions on how to install.

I'd recommend getting a handle on using conda if you are new to bioinformatics. It's incredibly useful.

However, if you just want to get off the ground and moving, the easiest way to do that would be to go the the releases page and download the binary (or wget <url> if you're on a server / cluster), and then then rename it with mv <name of download> perbase, then chmod +x perbase to make it executable. You can put it somewhere that is in your $PATH so it can be used from anywhere.

Alternatively, you can install rust (here), then run cargo install perbase which will compile it from source on your system. There's a chance it could run into issues requiring zlib and git on your system, so I'd recommend using conda or the pre-built binary for the least friction.

JMNGLS commented 1 year ago

Thank you Seth! you've given me a good start of things to try!

Thank you for making and maintaining this tool!

Jessie

On Wed, Sep 21, 2022, 3:40 PM Seth @.***> wrote:

Hi! Thanks for making an issue! Checkout the "Installation" section of the readme for instructions on how to install.

I'd recommend getting a handle on using conda if you are new to bioinformatics. It's incredibly useful.

However, if you just want to get off the ground and moving, the easiest way to do that would be to go the the releases https://github.com/sstadick/perbase/releases/tag/v0.8.5 page and download the binary (or wget if you're on a server / cluster), and then then rename it with mv perbase, then chmod +x perbase to make it executable. You can put it somewhere that is in your $PATH so it can be used from anywhere.

Alternatively, you can install rust (here https://www.rust-lang.org/tools/install), then run cargo install perbase which will compile it from source on your system. There's a chance it could run into issues requiring zlib and git on your system, so I'd recommend using conda or the pre-built binary for the least friction.

— Reply to this email directly, view it on GitHub https://github.com/sstadick/perbase/issues/56#issuecomment-1254306206, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3GP2WNOTZMGLQMBJYP5MMTV7OFEVANCNFSM6AAAAAAQSIZJRI . You are receiving this because you authored the thread.Message ID: @.***>

sstadick commented 1 year ago

@JMNGLS - you're welcome! I'm going to close this for now, but feel free to re-open if you run into issues.