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guigolab / FA-nf

Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow
GNU General Public License v3.0
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Quick Start #1

Closed rlebron-bioinfo closed 2 years ago

rlebron-bioinfo commented 3 years ago

Hi,

Nice pipeline. Could you please provide step by step instructions on how to build the image (including third-party images like sigtarp and ipscan), how to set up the pipeline and how to run it with the test datasets? I'm trying to do it myself, but mostly I'm having problems building the sigtarp and ipscan images. Thanks in advance.

Best regards, Ricardo Lebrón

toniher commented 3 years ago

Hello Ricardo, first of all, apologies for the delay answering you. I have improved a bit the documentation of Interproscan and Sigtarp container images. Let me know if you get stuck at some point. Including privative software in these cases may not be straightforward, since you need to get each different program through their specific ways before. In any case, since this can be an issue to other potential users, I have included the option to generate an Interproscan open image, and I also have modified the pipeline to include an option for skipping analyses with Signal & TargetP (sigtarp container images).

toniher commented 2 years ago

Several other improvements were made in the Interproscan image, and external repositories have been added as submodules in the repository. Please do not hesitate to open any additional ticket for any other specific issue.