Installation problem

[sajjadasaf]

(base) omic@omic-Precision-7920-Tower:/mir-seek$ module load snakemake singularity
module: command not found
(base) omic@omic-Precision-7920-Tower:/mir-seek$

[skchronicles]

Hey @sajjadasaf,

I hope you are having a good day!

The module load statments are examples of how you would add snakemake and singularity to your $PATH prior to execution.

This will vary depending on how your system was setup. If snakemake and singularity are already in your $PATH, you do not need to run that command.

These are the only two dependencies of the pipeline. If they are not installed, please reach out to a sysadmin to have these installed on your system. It is also worth noting that the pipeline only supports snakemake versions 7 and below.

If you have any additional questions feel free to reach out.

Best,
@skchronicles

[sajjadasaf]

please guide me what is wrong hereŷ
snakemake.log

command
(base) omic@omic-Precision-7920-Tower:~/mir-seek$ python mir-seek run --input /home/omic/mir-seek/*.gz --output /home/omic/SmallRNA/new --genome mm10 --mode local

[skchronicles]

Can you check what version of snakemake you are using?

snakemake --version

It appears you are using a version greater than 7.

[sajjadasaf]

thank you for your prompt reply. I install snakemake version 6.10 and run the pipeline and got the following error

akemake) omic@omic-Precision-7920-Tower:~/mir-seek$ python mir-seek run --input /home/omic/mir-seek/*.gz --output /home/omic/SmallRNA/new --genome mm10 --mode local
mir-seek (0.3.1)

Running mir-seek pipeline in 'local' mode...
mir-seek pipeline failed. Please see /home/omic/SmallRNA/new/logfiles/snakemake.log for more information.
(snakemake) omic@omic-Precision-7920-Tower:~/mir-seek$

@
snakemake.log

[sajjadasaf]

This pipeline work only with human and mouse database? or we can use other genome as well. I want to use Arabidopsis as reference genome for my data.