miga-base 1.4.2.0 → 1.4.2.4

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Files changed (7) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/cli/action/init/files_helper.rb +26 -5
  3. data/lib/miga/version.rb +2 -2
  4. data/scripts/mytaxa.bash +20 -13
  5. data/scripts/mytaxa_scan.bash +15 -8
  6. data/utils/requirements.txt +1 -1
  7. metadata +2 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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- data.tar.gz: 660ef6d7112c8b12b931fa0d8e664844f347f402c719933158ee0b4bdc227980
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+ metadata.gz: 5e0cb44349d861128c762b5285e8013f3086283c9a86e9e34197d3b37a6ed3e6
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- metadata.gz: 71e20e279276398703394ac2ddd1beac990537be238eeed71a9ae600c289a7b0a3f73b1420b3157851be5b0a289edba16b56e56a9abbc67e69e1b02c8dedc669
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- data.tar.gz: a6eb029e8c30f07510a54af8adb96e64b49eceadf8720a1483c8bc6a535b39d3cea9fddc17435aea1185e78746a2447ccd4bc8947648f4bdfbdbe77d82b19ae9
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+ metadata.gz: c0b2768551937f51919e74e7df35790d957418facc0498db6752662d8192d6c5c6fdd59b9ab5eec91e4d345675ed47e5154077a03722d84a79ea32d5501f1afb
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+ data.tar.gz: 5e4cb5dc6ad5c82cde159e3ff854111659d8b7c0d5b665a86a54757dc43cd95284dd97f870d921f37bd3711391669ae990282c9bbee8f8df832718afdd5292d6
data/lib/miga/cli/action/init/files_helper.rb CHANGED
@@ -64,12 +64,33 @@ module MiGA::Cli::Action::Init::FilesHelper
64
64
 
65
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  def check_mytaxa_scores(paths)
66
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  cli.print 'Looking for MyTaxa scores... '
67
- mt = File.dirname(paths['MyTaxa'])
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- unless Dir.exist?(File.join(mt, 'db'))
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- cli.puts "no\nExecute 'python2 #{mt}/utils/download_db.py'"
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- raise 'Incomplete MyTaxa installation'
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+ arch = 'mytaxa_db.tar.gz'
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+ mt = File.dirname(paths['MyTaxa'])
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+ mt_db = File.join(mt, 'db')
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+ mt_db_1 = File.join(mt_db, 'ncbiSciNames.lib')
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+ miga_db = File.join(ENV['MIGA_HOME'], '.miga_db', 'mytaxa')
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+ home_db = File.join(miga_db, 'db')
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+ home_db_1 = File.join(home_db, 'ncbiSciNames.lib')
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+
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+ if File.exist?(home_db_1)
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+ cli.puts 'yes'
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+ elsif File.exist?(mt_db_1)
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+ cli.puts 'yes, sym-linking'
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+ FileUtils.mkdir_p(miga_db)
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+ File.symlink(mt_db, home_db)
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+ else
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+ cli.puts 'no, downloading'
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+ MiGA::MiGA.download_file_ftp(
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+ :miga_dist, arch, File.join(miga_db, arch)
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+ ) { |n, size| cli.advance("#{arch}:", n, size) }
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+ cmd = <<~CMD
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+ cd #{miga_db.shellescape} \
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+ && tar zxf #{arch.shellescape} \
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+ && rm #{arch.shellescape}
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+ CMD
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+ run_cmd(cli, cmd, source: nil)
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+ cli.puts
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  end
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- cli.puts 'yes'
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  end
74
95
 
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  def check_mytaxa_database(paths)
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
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  # - String indicating release status:
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  # - rc* release candidate, not released as gem
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  # - [0-9]+ stable release, released as gem
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- VERSION = [1.4, 2, 0].freeze
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+ VERSION = [1.4, 2, 4].freeze
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  ##
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  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
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  ##
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  # Date of the current gem relese.
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- VERSION_DATE = Date.new(2026, 3, 19)
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+ VERSION_DATE = Date.new(2026, 4, 28)
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  ##
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  # References of MiGA
data/scripts/mytaxa.bash CHANGED
@@ -27,14 +27,21 @@ else
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  "no such file or directory" >&2
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  exit 1
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  fi
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- if [[ ! -d "$MT/db" ]] ; then
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- echo "Cannot locate the MyTaxa index: $MT/db:" \
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- "no such file or directory" >&2
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- exit 1
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+ if [[ -d "$MYTAXA_DB" ]] ; then
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+ echo "Using MYTAXA_DB=$MYTAXA_DB"
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+ elif [[ -d "$MIGA_HOME/.miga_db/mytaxa/db" ]] ; then
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+ export MYTAXA_DB="$MIGA_HOME/.miga_db/mytaxa/db"
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+ elif [[ -d "$MT/db" ]] ; then
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+ export MYTAXA_DB="$MT/db"
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+ else
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+ echo "Cannot locate the MyTaxa scores: rerun 'miga init'" >&2
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+ exit 1
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  fi
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- if [[ ! -d "$MT/utils" ]] ; then
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- echo "Cannot locate the MyTaxa utilities: $MT/utils:" \
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- "no such file or directory" >&2
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+ MT_UTILS="$MT/utils"
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+ [[ -n "$CONDA_PREFIX" && ! -d "$MT_UTILS" ]] \
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+ && MT_UTILS="$CONDA_PREFIX/share/mytaxa/utils"
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+ if [[ ! -d "$MT_UTILS" ]] ; then
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+ echo "Cannot locate the MyTaxa utilities: $MT_UTILS" >&2
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  exit 1
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  fi
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@@ -54,30 +61,30 @@ else
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  && gunzip "../../../06.cds/$DATASET.gff3.gz"
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  if [[ -e "../../../06.cds/$DATASET.gff2" ]] ; then
56
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  # GFF2
57
- perl "$MT/utils/infile_convert.pl" -f gff2 \
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+ perl "$MT_UTILS/infile_convert.pl" -f gff2 \
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  "../../../06.cds/$DATASET.gff2" "$DATASET.blast" \
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  | sort -k 13 > "$DATASET.mytaxain"
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  "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
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- perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
68
+ perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
62
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  -g "../../../06.cds/$DATASET.gff2" -f gff2 \
63
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  -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
64
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  -K "$DATASET.mytaxa.krona" -u
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  elif [[ -e "../../../06.cds/$DATASET.gff3" ]] ; then
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  # GFF3
67
- perl "$MT/utils/infile_convert.pl" -f gff3 \
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+ perl "$MT_UTILS/infile_convert.pl" -f gff3 \
68
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  "../../../06.cds/$DATASET.gff3" "$DATASET.blast" | sort -k 13 \
69
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  > "$DATASET.mytaxain"
70
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  "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
71
- perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
78
+ perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
72
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  -g "../../../06.cds/$DATASET.gff3" -f gff3 \
73
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  -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
74
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  -K "$DATASET.mytaxa.krona" -u
75
82
  else
76
83
  # No GFF
77
- perl "$MT/utils/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
84
+ perl "$MT_UTILS/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
78
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  | sort -k 13 > "$DATASET.mytaxain"
79
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  "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
80
- perl "$MT/utils/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
87
+ perl "$MT_UTILS/MyTaxa.distribution.pl" -m "$DATASET.mytaxa" \
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  -I "$DATASET.mytaxa.innominate" -G "$DATASET.mytaxa.genes" \
82
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  -K "$DATASET.mytaxa.krona" -u
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  fi
data/scripts/mytaxa_scan.bash CHANGED
@@ -26,14 +26,21 @@ else
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  "no such file or directory" >&2
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  exit 1
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  fi
29
- if [[ ! -d "$MT/db" ]] ; then
30
- echo "Cannot locate the MyTaxa index: $MT/db:" \
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- "no such file or directory" >&2
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- exit 1
29
+ if [[ -d "$MYTAXA_DB" ]] ; then
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+ echo "Using MYTAXA_DB=$MYTAXA_DB"
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+ elif [[ -d "$MIGA_HOME/.miga_db/mytaxa/db" ]] ; then
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+ export MYTAXA_DB="$MIGA_HOME/.miga_db/mytaxa/db"
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+ elif [[ -d "$MT/db" ]] ; then
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+ export MYTAXA_DB="$MT/db"
35
+ else
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+ echo "Cannot locate the MyTaxa scores: rerun 'miga init'" >&2
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+ exit 1
33
38
  fi
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- if [[ ! -d "$MT/utils" ]] ; then
35
- echo "Cannot locate the MyTaxa utilities: $MT/utils:" \
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- "no such file or directory" >&2
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+ MT_UTILS="$MT/utils"
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+ [[ -n "$CONDA_PREFIX" && ! -d "$MT_UTILS" ]] \
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+ && MT_UTILS="$CONDA_PREFIX/share/mytaxa/utils"
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+ if [[ ! -d "$MT_UTILS" ]] ; then
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+ echo "Cannot locate the MyTaxa utilities: $MT_UTILS" >&2
37
44
  exit 1
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  fi
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46
 
@@ -51,7 +58,7 @@ else
51
58
  fi
52
59
 
53
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  # Prepare MyTaxa input, execute MyTaxa, and generate profiles
54
- perl "$MT/utils/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
61
+ perl "$MT_UTILS/infile_convert.pl" -f no "LOREM_IPSUM" "$DATASET.blast" \
55
62
  | sort -k 13 > "$DATASET.mytaxain"
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63
  "$MT/MyTaxa" "$DATASET.mytaxain" "$DATASET.mytaxa" "0.5"
57
64
  fi
data/utils/requirements.txt CHANGED
@@ -18,6 +18,6 @@ Seqtk (reads) seqtk https://github.com/lh3/seqtk
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  Fastp (reads) fastp https://github.com/OpenGene/fastp
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  SPADES (reads) spades.py https://ablab.github.io/spades/ Required version: 3+
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  Temurin (rdp) java https://adoptium.net/ Any Java VM would work
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- MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
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+ MyTaxa (mytaxa) MyTaxa http://github.com/bio-miga/mytaxa Required version: 1.2+
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  Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
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  tRNAscan-SE tRNAscan-SE http://trna.ucsc.edu/tRNAscan-SE/ Required version: 2+
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
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3
  version: !ruby/object:Gem::Version
4
- version: 1.4.2.0
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+ version: 1.4.2.4
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  platform: ruby
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  authors:
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7
  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2026-03-19 00:00:00.000000000 Z
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+ date: 2026-04-28 00:00:00.000000000 Z
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12
  dependencies:
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  - !ruby/object:Gem::Dependency
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14
  name: daemons