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Welcome to the MarpoDB wiki!

Here we provide instructions for installation, compilation and running of the server, including troubleshooting sections for "difficult" libraries and software.

For the publication, see https://doi.org/10.1093/pcp/pcw201.

This Wiki is divided into three sections:

###Dependencies

Basically everything you will need to install/have for running the pipeline. For starters, be sure to have enough space, since some databases are very large if they aren't filtered by taxonomy. A rough estimate would be between 50 Gb to 100 Gb...

###Data compilation

In this section you will take two input files, namely you genome and transcriptome, place it on the data folder and run scripts that will predict ORFs and map those transcripts to the genome. Gene-features will be generated for each of those transcripts and will be included in the database. Afterwards, those ORFs containing entries will be retrieved for annotation and filtering by annotation quality, and then loaded to the database.

Depending on you dataset this section might take a LOT of time to run, specially if you did not filter you target databases (Uniprot) by taxonomy. For a 30K transcriptome it might even take a couple of weeks if you have limited resources to allocate...

###Server setup

Lock and load. Assuming everything went well, all whats left is to run the server and navigate to your server address. Common issues might be ports being closed.