miga-base 1.3.15.1 → 1.3.15.2

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data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
12
12
  # - String indicating release status:
13
13
  # - rc* release candidate, not released as gem
14
14
  # - [0-9]+ stable release, released as gem
15
- VERSION = [1.3, 15, 1].freeze
15
+ VERSION = [1.3, 15, 2].freeze
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16
 
17
17
  ##
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18
  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
20
20
 
21
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  ##
22
22
  # Date of the current gem relese.
23
- VERSION_DATE = Date.new(2024, 5, 6)
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+ VERSION_DATE = Date.new(2024, 5, 21)
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  ##
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  # References of MiGA
data/scripts/cds.bash CHANGED
@@ -64,7 +64,7 @@ fi
64
64
 
65
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  # Gzip
66
66
  for ext in gff3 faa fna ; do
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- [[ -e "$DATASET.$ext" ]] && gzip -9 -f "$DATASET.$ext"
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+ [[ -e "$DATASET.$ext" ]] && gzip -9f "$DATASET.$ext"
68
68
  done
69
69
 
70
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  # Finalize
data/scripts/miga.bash CHANGED
@@ -15,6 +15,11 @@ function exists { [[ -e "$1" ]] ; }
15
15
  # Evaluates if the first passed argument is a function
16
16
  function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
17
17
 
18
+ # Override gzip with pigz (if available)
19
+ if which -s pigz ; then
20
+ function gzip { pigz -p ${CORES:-2} "$@" ; }
21
+ fi
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+
18
23
  # Initiate a project-wide run
19
24
  function miga_start_project_step {
20
25
  local dir="$1"
data/scripts/mytaxa.bash CHANGED
@@ -86,12 +86,10 @@ else
86
86
  ktImportText -o "$DATASET.html" -n biota "$DATASET.mytaxa.krona,$DATASET"
87
87
 
88
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  # Gzip and cleanup
89
- [[ -e "../../../06.cds/$DATASET.gff2" ]] \
90
- && gzip -9 -f "../../../06.cds/$DATASET.gff2"
91
- [[ -e "../../../06.cds/$DATASET.gff3" ]] \
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- && gzip -9 -f "../../../06.cds/$DATASET.gff3"
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- gzip -9 -f "$DATASET.mytaxain"
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- gzip -9 -f "$DATASET.blast"
89
+ for i in "../../../06.cds/$DATASET.gff2" "../../../06.cds/$DATASET.gff3" \
90
+ "$DATASET.mytaxain" "$DATASET.blast" ; do
91
+ [[ -e $i ]] && gzip -9f $i
92
+ done
95
93
  rm "$DATASET.daa"
96
94
  fi
97
95
 
@@ -72,7 +72,7 @@ else
72
72
  awk "NR==$win" "$DATASET.wintax.genes" | tr "\\t" "\\n" \
73
73
  > "$DATASET.reg/$i.ids"
74
74
  if [[ "$FAA" == *.gz ]] ; then
75
- gzip -c -d "$FAA" \
75
+ gzip -cd "$FAA" \
76
76
  | FastA.filter.pl -q "$DATASET.reg/$i.ids" /dev/stdin \
77
77
  > "$DATASET.reg/$i.faa"
78
78
  else
@@ -81,8 +81,7 @@ else
81
81
  fi
82
82
  done
83
83
  # Archive regions
84
- tar -cf "$DATASET.reg.tar" "$DATASET.reg"
85
- gzip -9 "$DATASET.reg.tar"
84
+ tar -c "$DATASET.reg" | gzip -9c > "$DATASET.reg.tar.gz"
86
85
  rm -r "$DATASET.reg"
87
86
  fi
88
87
 
@@ -91,7 +90,7 @@ else
91
90
  [[ -e "$DATASET.$x" ]] && rm "$DATASET.$x"
92
91
  done
93
92
  [[ -s "$DATASET.mytaxa" && ! -s "$DATASET.mytaxa.gz" ]] \
94
- && gzip -9 -f "$DATASET.mytaxa"
93
+ && gzip -9f "$DATASET.mytaxa"
95
94
  fi
96
95
 
97
96
  fi
data/scripts/ssu.bash CHANGED
@@ -59,7 +59,7 @@ if [[ -s $fa ]] ; then
59
59
 
60
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  # Gzip
61
61
  for x in gff ssu.all.fa rdp.tsv trna.txt ; do
62
- [[ -e "${DATASET}.${x}" ]] && gzip -9 -f "${DATASET}.${x}"
62
+ [[ -e "${DATASET}.${x}" ]] && gzip -9f "${DATASET}.${x}"
63
63
  done
64
64
  fi
65
65
 
@@ -30,7 +30,8 @@ FastQ.tag.rb -i "$in1" -p "$b-" -s "/1" -o "$b.1.fastq.gz"
30
30
  [[ -e "$in2" ]] && FastQ.tag.rb -i "$in2" -p "$b-" -s "/2" -o "$b.2.fastq.gz"
31
31
 
32
32
  # Multitrim
33
- CMD="multitrim.py --zip gzip --level 9 --threads $CORES -o $b"
33
+ CMD="multitrim.py --level 9 --threads $CORES -o $b"
34
+ which -s pigz && CMD="$CMD --zip pigz"
34
35
  if [[ -s "$b.2.fastq.gz" ]] ; then
35
36
  # Paired
36
37
  $CMD -1 "$b.1.fastq.gz" -2 "$b.2.fastq.gz"
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.3.15.1
4
+ version: 1.3.15.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Luis M. Rodriguez-R
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2024-05-06 00:00:00.000000000 Z
11
+ date: 2024-05-21 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons