linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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Explanation for docker command #128

Closed blueevee closed 1 year ago

blueevee commented 1 year ago

Hi! I'm trying to execute dbcan on docker and getting in some trouble understanding the command. I am not an expert on anything of this, but I already sold out all my ideas. I understand that I need to put my host path to bind a volume in docker path, I need also my file and a output directory so my last attempt was this: docker run --name dbcan2 -v C:/Users/evelyn.ferreira/Documents/eevee/estudos/FACULDADE/TCC/plasticome/plasticome/genomes:/genomes -it haidyi/run_dbcan:latest python run_dbcan.py /genomes/123.faa prok --out_dir /genomes But I am getting this error, like it can't create the output folder and can't find the file to execute:

image

I really want to understand how I must have to put the input file, I already try the absolute host path, and relative path, but I'm always getting the error "No such file or directory". My unique successful attempt was when use the sample file "EscheriaColiK12MG1655.fna", but I really think that its using the example file inside the container and not use my created volume folder :/ docker container run -ti --name dbcan-2 -v C:/Users/evelyn.ferreira/Documents/eevee/estudos/FACULDADE/TCC/plasticome/plasticome/genomes:/app/genomes haidyi/run_dbcan:latest EscheriaColiK12MG1655.fna protein --out_dir teste_2

Just to show that my volume is inside the container too: image

I really appreciate some help with it!

linnabrown commented 1 year ago

Sorry I will have long drive tmr. I will respond I next week thx

blueevee commented 1 year ago

Oh thank you very much, I hope to hear from you soon good drive!

blueevee commented 1 year ago

I rewrote my function and changed my files, and now it works for me!!!