This gist will let you efficiently install all the R packages and data suggested for the flyconnectome team
Start a clean R session and do:
if(!require("devtools")) install.packages("devtools")
devtools::source_gist("fdd1e5b6e009ff49e66be466a104fd92", filename = "install_flyconnectome_all.R")| # we need devtools for additional installs | |
| if(!require("devtools")) install.packages("devtools") | |
| message("installing packages") | |
| devtools::source_gist("fdd1e5b6e009ff49e66be466a104fd92", filename = "install_flyconnectome_packages.R") | |
| devtools::source_gist("fdd1e5b6e009ff49e66be466a104fd92", filename = "install_flyconnectome_data.R") |
| message("Setting up flycircuit dataset including pre-computed NBLAST scores") | |
| devtools::source_gist("bbaf5d53353b3944c090", filename = "FlyCircuitStartupNat.R") | |
| message("Downloading flycircuit neurons for de novo NBLAST - this could take 15m to overnight") | |
| library(flycircuit) | |
| dps<-read.neuronlistfh("http://flybrain.mrc-lmb.cam.ac.uk/si/nblast/flycircuit/dpscanon.rds", | |
| localdir=getOption('flycircuit.datadir')) | |
| remotesync(dps,download.missing = TRUE) |
| # we need devtools for additional installs | |
| if(!require("devtools")) install.packages("devtools") | |
| # this will install all the regular nat packages | |
| devtools::source_gist("39a1182f726989db7e03", filename="install_all_nat.R") | |
| # elmr will bring in all the other packages we need | |
| devtools::install_github("jefferis/elmr", dependencies=TRUE) |