adomingues

```{r }
library("recount3")
library("data.table")
library("magrittr")
library("DESeq2")

rse <- recount3::create_rse_manual(
    project = "ERP010060",
    project_home = "data_sources/sra",
    organism = "human",

adomingues

find . -maxdepth 2 -name ".hg" -type d

## convert hg to git
pip install mercurial ## apt install did not work with the conversion tool

## install conversion tool
mkdir -p ~/bin
cd ~/bin/
git clone https://github.com/frej/fast-export.git

adomingues

parent=$(pwd)
for repo in $(find ${parent} -maxdepth 2 -name ".git" -type d | sed 's/.git//'); do
	cd ${repo} 
	n=$(git branch | wc -l)
	if [[ ${n} -gt 1 ]]; then
		echo ${repo}
	fi	
	cd ${parent}
done

adomingues

cd .ssh/
mkdir -p ~/.ssh/backup_keys

## backup current keys just in case
for k in id_*; do
	cp $k backup_keys/$k"_bak_$(date +"%m_%d_%Y")"
done

## it will ask for a password for every key file
for k in $(ls id_* | grep -v pub); do

adomingues

sessionInfo()                                                                   R version 3.5.1 (2018-07-02) 
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /fsimb/common/tools/R/3.5.1/lib/R/lib/libRblas.so
LAPACK: /fsimb/common/tools/R/3.5.1/lib/R/lib/libRlapack.so
                                                                                                                                                                                         
locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C                                                                                                                                             

adomingues

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:

adomingues

## set default repository
options(repos = "http://cran.rstudio.com")

## install packages if missing
suppressMessages(if (!require("devtools")) utils::install.packages("devtools"))
suppressMessages(if (!require("rdoc")) devtools::install_github("mdequeljoe/rdoc"))
suppressMessages(if (!require("prettycode")) utils::install.packages("prettycode"))

## prettify the docs
rdoc::use_rdoc()

adomingues

# install the Rsamtools package if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
 
# load the library
library(Rsamtools)

# specify the bam file you want to import
bamFile <- "test.bam"

adomingues

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

adomingues

samples <- structure(list(sample = structure(c(3L, 4L, 5L, 6L, 7L, 8L, 9L, 
10L, 1L, 2L, 14L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 20L, 21L, 
22L, 23L, 23L, 24L, 25L, 11L, 12L, 13L), .Label = c("wt_Fish_10dpf_rep1_mRNA", 
"wt_Fish_10dpf_rep2_mRNA", "wt_Fish_1dpf_rep1_mRNA", "wt_Fish_1dpf_rep2_mRNA", 
"wt_Fish_2dpf_rep1_mRNA", "wt_Fish_2dpf_rep2_mRNA", "wt_Fish_3dpf_rep1_mRNA", 
"wt_Fish_3dpf_rep2_mRNA", "wt_Fish_6dpf_rep1_mRNA", "wt_Fish_6dpf_rep2_mRNA", 
"wt_PGCs_10dpf_rep1_mRNA", "wt_PGCs_10dpf_rep2_mRNA", "wt_PGCs_10dpf_rep3_mRNA", 
"wt_PGCs_1dpf_rep1_mRNA", "wt_PGCs_1dpf_rep2_mRNA", "wt_PGCs_1dpf_rep3_mRNA", 
"wt_PGCs_2dpf_rep1_mRNA", "wt_PGCs_2dpf_rep2_mRNA", "wt_PGCs_2dpf_rep3_mRNA", 
"wt_PGCs_3dpf_rep1_mRNA", "wt_PGCs_3dpf_rep2_mRNA", "wt_PGCs_3dpf_rep3_mRNA",