Bowtie2 missing in Bismark container

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BioContainers specifications

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Bowtie2 missing in Bismark container #100

Closed stolarczyk closed 5 years ago

stolarczyk commented 5 years ago

Bowtie2 software is not installed in the Bismark container: quay.io/biocontainers/bismark:0.18.1--pl5.22.0. Consquently, the bismark_genome_preparation --bowtie2 command execution results in the following error:

Can't exec "bowtie2-build": No such file or directory at /usr/local/bin/bismark_genome_preparation line 178, <IN> line 75966.
Parent process: Failed to build index

Please see this issue for more detail

Thank you!

bgruening commented 5 years ago

@michalstolarczyk not sure what happened to the 0.18.1 version. Do you need this specific one? I think the containers are ok from everything quay.io/biocontainers/bismark:0.19.0--1 onwards ...

stolarczyk commented 5 years ago

No, I do not need this specific version. It's just the first one that pops up in the search results. Tried the latest version and it works.

Thanks!