bowtie2

[paupaiz]

Hi Dr. Aboukhalil, Thank you for building sandbox.bio! I am trying the bowtie2 tutorial which worked around a week ago but now I don't have a path set in $REF and the aligner doesn't work:

Not sure if it is related but I created an account and signed in (that's the only difference from last time I tried).

[robertaboukhalil]

Hi @paupaiz, thanks for reaching out!

Have you tried refreshing the page and seeing if echo $REF works?

If not, can you try typing the command:

REF=/bowtie2/example/index/lambda_virus; REF_FASTA=/bowtie2/example/reference/lambda_virus.fa

and seeing if it works after that?

[paupaiz]

It worked after typing that command!