'How to run Hisat2 in Google colab?

I am trying to run this code on Google colab, but I keep having errors

hisat2Ref=/mnt/c/3adera-RNA/mkr-index/mkr1
hisat2 -x ${hisat2Ref} \
     -U IL1R_Th17_PreTrans_R1.fastq.gz|
        samtools view -bh - |
        samtools sort - > IL1R_Th17_PreTrans_R1.bam
        samtools index IL1R_Th17_PreTrans_R1.bam
htseq-count -f bam IL1R_Th17_PreTrans_R1.bam mkr-mus-genome.gtf.gz > IL1R_Th17_PreTrans_R1.txt

Any help is appreciated.

google-colaboratoryrna-seq


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