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snandiDS / prokseq-v2.0

MIT License
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Problem with docker #2

Closed marcelladane closed 2 years ago

marcelladane commented 3 years ago

Hello, I tried to install your pipeline using the docker image but it says that salmon was not found when I try to run it with the trial files. And therefore the pipeline doesn't complete.

Can you advise on how to solve the issue?

Best regards Marcela

marcelladane commented 3 years ago

Reinstallation worked. But still without salmon, it ran only bowtie2. How can I install salmon apart in the docker?

Also, the following error is showing during the run and may cause future problems: " samtools mpileup option S is functional, but deprecated. "

snandiDS commented 3 years ago

Hi, to run the salmon, use the parameter and sample file for salmon like param.salmon.PE or samples.salmon. If you run bowtie by default it does not look for salmon and shows the error message.