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This question is mostly for Eric, but I'd take advice from anyone.

Since I'm trying to analyze bisulfite sequencing data and need to use Bismark I was checking in the discovery environment to see if it had been integrated into iPlant. No luck, it seems:

However, I then searched the help forums and I saw a post that mentioned that the actual tool may be installed in the system, but no app had been created yet. So, I went to the app creation screen to look for Bismark as a "tool."

Apparently it is in there. However, the version is quite old. It's now up to 0.13.1 as of last month.

Do you think it would be worthwhile to try to have the newer version installed in iPlant, and an app created, or to just use the HPC (if the program is even installed on that)? I'm in the process of installing it on my home computer to test out things that way.


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  1. Hi Jeffrey,

    Please search the HPC Category in the DE for Bismark 0.13.1. We have recently integrated this tool leveraging the HPC resources available to us. We also have Bismark_meythlation_extractor 0.13.1 and Bismark_genome_preparation 0.13.1 available in this category. Please let me know if you are unable to view these, and I will double check the permissions.

    1. I didn't realize these were under a separate section. Yes, I can see them in there. Thank you for the help! 

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