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liulab-dfci / MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline
GNU General Public License v3.0
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A bug in Snakemake/scRNA/Snakefile #110

Closed QiangTU closed 3 years ago

QiangTU commented 3 years ago

Hi, I am using v1.3.1, and found a bug in Snakemake/scRNA/Snakefile:

shell:
        "python " + SCRIPT_PATH + "/lisa_path.py --species {params.species} --input {params.lisadir} "
        "Rscript " + RSCRIPT_PATH + "/scRNAseq_pipe.R --expression {params.expression} --species {params.species} "
        "--prefix {params.outpre} --signature {params.signature} "
        "--outdir {params.outdir} --thread {threads}"

There should be a ; at the end of the lisa_path line.

When I manually fixed this problem, the pipeline complained: 

lisa: error: invalid choice: 'unpack' (choose from 'oneshot', 'multi', 'regions', 'coverage', 'download', 'install', 'run-tests')

So there might be some more problems with lisa_path.py? It only does unpack.

crazyhottommy commented 3 years ago

it worked when we tested it, but when you installed v1.3.1, lisa2 get updated and you had the latest version of lisa2 so it breaks. we will specify the version of lisa2 in the next release to fix this. Thanks for the report. we should have one release this week.

QiangTU commented 3 years ago

Thanks a lot! I installed v1.3.1 by mama, how can I upgrade it to v1.3.2?

crazyhottommy commented 3 years ago

It is better to create a new env for the new version. I will reply here when it is out. or you can try mamba update. I did not test.

crazyhottommy commented 3 years ago

@QiangTU the new version fixed this. mamba create -n MAESTRO maestro=1.3.2 -c liulab-dfci