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Weeks-UNC / fpocketR

Program to find drug-like RNA-ligand binding pockets.
MIT License
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potential BUG: conda executable path #2

Open fryzjergda opened 7 months ago

fryzjergda commented 7 months ago

Hi, I was having trouble with running the fpocketR, and narrowed down the problem to posket.run_fpocket().

the bash command there is (line 100):

    bash_command = f'conda run -n fpocketR fpocket -f {pdb} -k {chain} -l {state} -m {m} -M {M} -i {i} -D {D} -A {A} -p {p} -w p'

In my case the program was unable to invoke conda, so I had to explicitly give it a path to my conda executable:

    conda_executable = "/home/user/miniconda3/bin/conda"
    bash_command = f'{conda_executable} run -n fpocketR fpocket -f {pdb} -k {chain} -l {state} -m {m} -M {M} -i {i} -D {D} -A {A} -p {p} -w p'

I don't know if this was specific to my case, but wanted to let you know about the potential bug.

Best, Tomasz

VonBoss commented 6 months ago

I haven't found a better way to implement the fpocket subprocess yet, hopefully, this isn't a widespread issue. Thanks