miga-base 1.2.2.0 → 1.2.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ab62d2e6d20aa126a5f455bd3b8159549d5c39b7b2e747587a0b0444a30d935a
-  data.tar.gz: 273671304affb6a21d1e4dc0374c4ff17edf39a96cba8893d2a666640ab1c7c9
+  metadata.gz: b13fbb5ae17b883dde03cec010e19649e09cecf2254e5bf9f4e8f9e5447d6445
+  data.tar.gz: a26e562d5517dbad291a4817c2c309f7472460a7e6c063a811a9949d060e7667
 SHA512:
-  metadata.gz: a157f0c4c52cfe4729eb5bda27900150153606b80f816a169ef18d6603b3fcd0ac03574cdbafbfcfe73e56a55ffbbf168a8c4316f066674ff6aebf6cef168500
-  data.tar.gz: 1a7b42d7dc75c5cac04f3408e6fba0e989d46ac63e926602c020e15340e24e8dc4694bf07b5f75ecc3a707db9d110d4a379841c426f7eb4a5670da5bcfa9642e
+  metadata.gz: e16918bfa39b28db6b057bc9794e8766a56cffe36bff47d29e8d57ef5dac7274fdec1369291c468123acf7dbb7c2002ec58e8e9b0715f01c1e508d355f0a74a8
+  data.tar.gz: 78217ee076fe60f36273e6ce8638a32cd4b117ffa524d2d7bc2d5286a179b40e4e8117d6eab617f73e5283ca57860f8197b1f9052be3f356acff8b116b50e2f7

data/lib/miga/cli/action/init/files_helper.rb

@@ -112,7 +112,7 @@ module MiGA::Cli::Action::Init::FilesHelper
           && tar zxf #{arch.shellescape} \
           && rm #{arch.shellescape}
       CMD
-      run_cmd(cmd, source: nil)
+      run_cmd(cli, cmd, source: nil)
       cli.puts
     end
   end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 2, 0].freeze
+  VERSION = [1.2, 2, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2021, 12, 12)
+  VERSION_DATE = Date.new(2022, 1, 27)
 
   ##
   # References of MiGA

data/utils/ref-tree.R

@@ -5,38 +5,43 @@
 #
 
 #= Load stuff
-argv <- commandArgs(trailingOnly=T)
+argv <- commandArgs(trailingOnly = TRUE)
 suppressPackageStartupMessages(library(ape))
-if(Sys.getenv('MIGA') == ''){
+if (Sys.getenv("MIGA") == "") {
   suppressPackageStartupMessages(library(enveomics.R))
-}else{
-  source(file.path(Sys.getenv('MIGA'),
-    'utils', 'enveomics', 'enveomics.R', 'R', 'df2dist.R'))
+} else {
+  source(
+    file.path(
+      Sys.getenv("MIGA"), "utils", "enveomics", "enveomics.R", "R", "df2dist.R"
+    )
+  )
 }
 inst <- c("phangorn", "phytools") %in% rownames(installed.packages())
-if(inst[1]){
+if (inst[1]) {
   suppressPackageStartupMessages(library(phangorn))
   reroot.fun <- midpoint
-}else if(inst[2]){
+} else if (inst[2]) {
   suppressPackageStartupMessages(library(phytools))
   reroot.fun <- midpoint.root
-}else{
+} else {
   reroot.fun <- function(x) return(x)
 }
 
 #= Main function
 ref_tree <- function(ani_file, out_base, q_dataset) {
-  a <- read.table(ani_file, sep="\t", header=TRUE, as.is=TRUE)
-  ani.d <- enve.df2dist(a[,1:3], default.d=0.9, max.sim=100)
+  a <- read.table(ani_file, sep = "\t", header = TRUE, as.is = TRUE)
+  ani.d <- enve.df2dist(a[, 1:3], default.d = 0.9, max.sim = 100)
   ani.ph <- reroot.fun(bionj(ani.d))
-  write.tree(ani.ph, paste(out_base, ".nwk", sep=""))
-  pdf(paste(out_base, ".nwk.pdf", sep=""), 7, 7)
-  plot(ani.ph, cex=1/3, type='fan',
-    tip.color=c('red', 'black')[ifelse(ani.ph$tip.label==q_dataset, 1, 2)])
+  write.tree(ani.ph, paste(out_base, ".nwk", sep = ""))
+  pdf(paste(out_base, ".nwk.pdf", sep = ""), 7, 7)
+  plot(
+    ani.ph, cex = 1/3, type = "fan",
+    tip.color = c("red", "black")[ifelse(ani.ph$tip.label == q_dataset, 1, 2)]
+  )
   add.scale.bar()
   dev.off()
 }
 
 #= Main
-ref_tree(ani_file=argv[1], out_base=argv[2], q_dataset=argv[3])
+ref_tree(ani_file = argv[1], out_base = argv[2], q_dataset = argv[3])
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.2.0
+  version: 1.2.2.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-12-12 00:00:00.000000000 Z
+date: 2022-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons