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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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SyntaxError in line 7 of Snakefile #117

Closed amufaamo closed 2 years ago

amufaamo commented 2 years ago

Hi, I try to run dropSeqPipe, but I got error

snakemake --cores 8 qc --e-conda --directory /dropSeqPipe/working_dir/ 

SyntaxError in line 7 of /dropSeqPipe/Snakefile:
invalid syntax

line 7 of Snakefile is singularity: is something wrong?

import pandas as pd
import os
import re
import glob
from snakemake.utils import validate, min_version

singularity:
    "shub://seb-mueller/singularity_dropSeqPipe:v04"

min_version("5.1.2")
nogay commented 2 years ago

Got the same error

nogay commented 2 years ago

I think it's got to do with snakemake version. I was using 'bioconda/linux-64::snakemake-3.13.3-py36_0' that I installed using conda by following the installation documentation.

After deactivating the environment and using the system snakemake (version 6.6.1) it worked. Well it kind of worked, now it says I don't have mamba package manager but that is probably another issue.

amufaamo commented 2 years ago

OK, I will re-install snakemake. I try it now.

amufaamo commented 2 years ago

Thank you it worked!! but I got new error. Close this issue, and build new issue. Thank you so much