vinisalazar

Final Work Product Report - GSoC 2022

Project: Refactoring of erddapy into separate core and object layers

Organization: Integrated Ocean Observing System (IOOS)
Contributor: Vini Salazar
Mentors:

• Mathew Biddle
• Filipe Fernandes
• Alex Kerney

Please see our mid-project blog post.

vinisalazar

viniws@woese:~/Code/deepvariant$ ./build-prereq.sh 
========== Load config settings.
========== [qua set 26 17:47:35 -03 2018] Stage 'Install the runtime packages' starting
========== Load config settings.
========== [qua set 26 17:47:35 -03 2018] Stage 'Misc setup' starting
========== [qua set 26 17:47:35 -03 2018] Stage 'Update package list' starting
E: The repository 'http://apt.postgresql.org/pub/repos/apt YOUR_UBUNTU_VERSION_HERE-pgdg Release' does not have a Release file.
E: The repository 'http://ppa.launchpad.net/gnome-terminator/ppa/ubuntu bionic Release' does not have a Release file.

vinisalazar

import pandas as pd
import matplotlib.pyplot as plt
import numpy as np

f = open('./sampling/25-01-17/stations_25-01-2017_RAW.cnv', 'r')
t = f.readlines()

f.close()

# creating lists for our headers, data, and variable names

vinisalazar

### Protocolo de análise - Comunidade microbiana da Lagoa da Conceição ###

This protocol was created to guarantee the transparency and reproducibility of the data analysis performed by the Group of Microbial Oceanography (GOM - UFSC) for the **Lagoa BioEnergy** project.

This analysis was conducted using the following computational tools: [PEAR](http://www.exelixis-lab.org/pear) (*v0.9.10*), [QIIME](http://qiime.org/) (*v1.9.1*), [USEARCH](http://www.drive5.com/usearch/) (*v7.0*), the [SILVA](https://www.arb-silva.de/) (*119*) database, all based on the protocol developed by the [Brazilian Microbiome Project](http://www.brmicrobiome.org/#!16s-profiling-pipeline-illumina/czxl) (**BMP**). We recommend consulting the BMP website to learn more about this analysis. You can find more complete information about these softwares on the references of the paper related to this document.

All of the following commands are typed on the Terminal app (bash):