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farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
https://gentb.hms.harvard.edu
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download a standalone version of GenTB #267

Open Ankitapal1995 opened 2 years ago

Ankitapal1995 commented 2 years ago

I have 4000 of M.tb genome and want to analyze their resistance. Could you please guide me to download a standalone version of GenTB?

mahafarhat commented 2 years ago

please see the standalone version here: https://github.com/farhat-lab/gentb-snakemake

On Mon, Jul 25, 2022 at 1:35 AM Ankitapal1995 @.***> wrote:

I have 4000 of M.tb genome and want to analyze their resistance. Could you please guide me to download a standalone version of GenTB?

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Ankitapal1995 commented 2 years ago

Thanks a lot.

Ankitapal1995 commented 2 years ago

when i am using conda env create -f envs/snakemake-gentb.yml for creating environment it is showing following error.

ResolvePackageNotFound:

gcc_impl_linux-64==7.5.0=hd420e75_6 gfortran_impl_linux-64==7.5.0=hdf63c60_6 gxx_impl_linux-64==7.5.0=hdf63c60_6 libgfortran-ng==7.5.0=hdf63c60_6 I installed above packages with same mentioned version using conda still showing same error.

mgro commented 2 years ago

What OS / version are you using? Can you try removing these libraries from the yml file and install the conda environment again?

Ankitapal1995 commented 2 years ago

I had tried both with centOS7 and ubuntu 16.04, both are showing above mentioned error. As you suggested, I removed those libraries from the yml file and tried installing it again. didn't work for me.

mgro commented 2 years ago

I would try next to start with a fresh conda environment and install the tools needed up to the prediction step (fastp, minimap2, samtools, pilon). Then you can try running the snakemake up to the step where the prediction matrices are generated (i.e. change the rule all part in the snake file):

rule all: input: expand("results/{sample}.matrix.pyrazinamide.csv", sample=SAMPLES)