miga-base 0.5.2.0 → 0.5.2.1
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- checksums.yaml +4 -4
- data/lib/miga/version.rb +2 -2
- data/scripts/essential_genes.bash +6 -6
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -1
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -1
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -1
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -1
- metadata +3 -4
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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|
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 4e63c0be19f4c1deb225b622ffae0d4745484c4e5e9e14433b588986bf6f7a5a
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4
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+
data.tar.gz: 609dfcbd7207f1a2a63dc76f9674357182734d19eaea1e26bb857286b2932e05
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5
5
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SHA512:
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|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
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|
6
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+
metadata.gz: fcc03a3382fbc0510773298e708ae42ebf0b16a565e5feedf6f31b732a86d1538cc6545428c69f7dd553aaaa79530b018f130d487091a45db07d6dc242790be3
|
|
7
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+
data.tar.gz: 3bebfccfff429d53b131e8f8716e9af51c61abd686267d496d1e0f71524edc85d91623e1b86d7202257edafaaf8d0089957fd87224524a7ef65e73f604d96173
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data/lib/miga/version.rb
CHANGED
|
@@ -10,7 +10,7 @@ module MiGA
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|
|
10
10
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# - Float representing the major.minor version.
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11
11
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# - Integer representing gem releases of the current version.
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12
12
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# - Integer representing minor changes that require new version number.
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13
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-
VERSION = [0.5, 2,
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|
13
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+
VERSION = [0.5, 2, 1]
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14
14
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15
15
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##
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16
16
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# Nickname for the current major.minor version.
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@@ -18,7 +18,7 @@ module MiGA
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18
18
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|
19
19
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##
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|
20
20
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# Date of the current gem release.
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|
21
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-
VERSION_DATE = Date.new(2020, 1,
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|
21
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+
VERSION_DATE = Date.new(2020, 1, 8)
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|
22
22
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23
23
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##
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|
24
24
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# Reference of MiGA.
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@@ -26,15 +26,15 @@ TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" \
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26
26
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--metadata "type" | awk '{print $2}')
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|
27
27
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COLL=$(miga about -P "$PROJECT" -m ess_coll)
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|
28
28
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[[ "$COLL" == "?" ]] && COLL=dupont_2012
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|
29
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-
CMD="HMM.essential.rb \
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|
30
|
-
-i '$FAA' -o '${DATASET}.ess.faa' -m '${DATASET}.ess/' \
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|
31
|
-
-t '$CORES' -r '$DATASET' --collection '$COLL'"
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|
32
29
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if [[ "$TYPE" == "metagenome" || "$TYPE" == "virome" ]] ; then
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|
33
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-
|
|
30
|
+
FLAGS="--metagenome"
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|
34
31
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else
|
|
35
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-
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|
32
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+
FLAGS="--alignments ${DATASET}.ess/proteins.aln"
|
|
36
33
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fi
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|
37
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-
|
|
34
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+
HMM.essential.rb \
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|
35
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+
-i "$FAA" -o "${DATASET}.ess.faa" -m "${DATASET}.ess/" \
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|
36
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+
-t "$CORES" -r "$DATASET" --collection "$COLL" $FLAGS \
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|
37
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+
> "${DATASET}.ess/log"
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38
38
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|
|
39
39
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# Reduce files
|
|
40
40
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if exists "$DATASET".ess/*.faa ; then
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@@ -1 +1 @@
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1
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-
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|
1
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+
../../Scripts/FastA.N50.pl
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@@ -1 +1 @@
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|
|
1
|
-
|
|
1
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+
../../Scripts/FastA.filterN.pl
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|
@@ -1 +1 @@
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|
|
1
|
-
|
|
1
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+
../../Scripts/FastA.length.pl
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@@ -1 +1 @@
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|
|
1
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-
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|
1
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+
../../Scripts/FastA.split.pl
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@@ -1 +1 @@
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|
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1
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-
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|
1
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+
../../enveomics.R
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metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
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--- !ruby/object:Gem::Specification
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|
2
2
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name: miga-base
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|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.5.2.
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|
4
|
+
version: 0.5.2.1
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|
5
5
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platform: ruby
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|
6
6
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authors:
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|
7
7
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- Luis M. Rodriguez-R
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|
8
8
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autorequire:
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|
9
9
|
bindir: bin
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|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2020-01-
|
|
11
|
+
date: 2020-01-08 00:00:00.000000000 Z
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|
12
12
|
dependencies:
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|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: daemons
|
|
@@ -515,8 +515,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
515
515
|
- !ruby/object:Gem::Version
|
|
516
516
|
version: '0'
|
|
517
517
|
requirements: []
|
|
518
|
-
|
|
519
|
-
rubygems_version: 2.7.6
|
|
518
|
+
rubygems_version: 3.0.3
|
|
520
519
|
signing_key:
|
|
521
520
|
specification_version: 4
|
|
522
521
|
summary: MiGA
|