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gbouras13 / hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
MIT License
108 stars 8 forks source link

[Feature request] Addding the option to write the database to a specific directory #60

Closed npbhavya closed 8 months ago

npbhavya commented 8 months ago

I am running the command, hybracter install -o temp -d hybracterDB

Running into the error 2024-03-13 10:17:42.184 | INFO | plassembler:download:1123 - Checking database installation at hybracterDB 2024-03-13 10:17:42.184 | ERROR | plassembler.utils.db:check_db_installation:43 - Directory hybracterDB already exists and force was not specified. Please specify -f or --force to overwrite hybracterDB

But -f option is only within plassembler, so adding -f to the above hybracter command is not being translated. So just adding -f option to the plassembler download rule would fix this.

I am not sure why the directory "hybracterDB" already exists since its the first time I am defining that directory

gbouras13 commented 8 months ago

This should be an easy fix @npbhavya thanks for raising it.

I think the cause is a Snakemake reason - it will make the output files/directories at the start of a rule so you always need -f.

George

gbouras13 commented 8 months ago

@npbhavya I've pushed a fix to the dev branch if you want to give it a go. Once it passes I will merge and release