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marschall-lab / panacus

Panacus is a tool for computing statistics for GFA-formatted pangenome graphs
MIT License
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What does the output content represent #3

Closed xuxingyubio closed 1 year ago

xuxingyubio commented 1 year ago

When I used the pangenome-growth command, I got a 5-column data, and what do the last three columns represent?When I build a sample file, I only need to write the sample name instead of using the haplotype form of sample name. 1.2. Is this a requirement for the sample file that was previously constructed as a pangenome?

danydoerr commented 1 year ago

Please use use the "ng" branch. It will be pushed to main any day now. I will also add a tutorial and documentation to the README. For now, please use https://hackmd.io/asojhSf-T8GOJOr9HQj_IA#Panacus for orientation. Since the file format changed a lot in this new version, I think your question will no longer be valid. If you have any questions, please post here.

1538501175 commented 1 year ago

How can I download Panacus? I couldn't find a download link on your latest webpage https://hackmd.io/asojhSf-T8GOJOr9HQj_IA#Panacus

danydoerr commented 1 year ago

At the moment, you can only download the source (make sure you're on the "ng" branch!) and then compile it yourself (cargo build --release). I'll make it soon (~2 weeks) available through conda.

1538501175 commented 1 year ago

Sorry to bother you again. I don't understand what the "ng" branch means. I was able to install pangenome-growth0.1 using the recommended command "cargo build --release" and successfully run it on animals pangenome. In your tutorial notes, you mentioned that it's already available on the course workstations, but I don't have access to those workstations.

danydoerr commented 1 year ago

Sure, I’m happy to help! Just do git branch ng && git pull origin ng you will be on the ng branch. Then recompile and you’re good to go. Note that panacea supports only Linux for now, but with the planned release it will also support MacOS. On 17.

danydoerr commented 1 year ago

Sorry, it's git checkout ng && git pull origin ng.

danydoerr commented 1 year ago

New version is now in main and finally released (including pre-compiled executables). I'm closing this issue now.