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zhxiaokang / RASflow

RNA-Seq analysis workflow
MIT License
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Can't run the examples #34

Closed antoniaprn closed 1 year ago

antoniaprn commented 1 year ago

Hi, thank you for your work. I'm just installed RASflow by the Conda environment with the yaml file env.yaml like the tutorial and tried to run the example changing the project name and even another sample, but keeping get the error in the first QC to stop that is nice: ‘snakemake’: No such file or directory and the outputs files don't appear.

This is how is my config_main.yaml characteristics was:

PROJECT: teste QC: yes # "yes" or "no" TRIMMED: no # "yes" or "no"? REFERENCE: genome # "genome" or "transcriptome" DEA: yes # "yes" or "no" VISUALIZE: no # "yes" or "no" READSPATH: data/example/fastq_pair METAFILE: configs/metadata.tsv END: pair NCORE: 40 OUTPUTPATH: data/output/teste # intermediate output. do not upload to github FINALOUTPUT: output/teste GENOME: data/example/ref/genome/Homo_sapiens.GRCh38.dna.chromosome.1.1.10M.fa ANNOTATION: data/example/ref/annotation/Homo_sapiens.GRCh38.93.1.1.10M.gtf ALIGNER: hisat2 COUNTER: featureCounts
alignmentQC: no # "yes" or "no" to specify whether you want to do alignment QC DEATOOL: DESeq2
PAIR: FALSE # Is this a pair test or not? ("TRUE" or "FALSE") CONTROL: ["Untreated"] TREAT: ["Dexamethasone"] obs.: a let false just for testing if goes.

FILTER: yesOrNo: FALSE # Filter out low expressed transcripts/genes or not? (TRUE or FALSE) It's better to be set to TRUE. FALSE is set as default only for testing fake toy data

zhxiaokang commented 1 year ago

Hi, I suppose that you have created the environment successfully, then snakemake should be there. The reason of this error could be that you are not in that environment.

To active the environment, use command conda activate rasflow (if you named the environment as 'rasflow'). The detailed explanation is on Page 3 of the Tutorial

antoniaprn commented 1 year ago

Yes, but I am in the environment that's why I can find out the problem.

zhxiaokang commented 1 year ago

Try conda list (Conda Doc here ) to check whether snakemake is there. If not, I suspect that the environment was not successfully created. Then either try creating the Conda environment again, or try using Docker