miga-base 1.0.5.1 → 1.0.5.5

Sign up to get free protection for your applications and to get access to all the features.
Files changed (7) hide show
  1. checksums.yaml +4 -4
  2. data/bin/miga-env +6 -0
  3. data/lib/miga/version.rb +2 -2
  4. data/scripts/miga.bash +2 -2
  5. data/scripts/mytaxa_scan.bash +1 -1
  6. data/utils/requirements.txt +7 -7
  7. metadata +3 -2
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: 9867b3df06290fb7eb25e10b39dd439c9db52d33c9beb3657e76b1f8da570c47
4
- data.tar.gz: a53428a16e8d34b48e0e889c54169f287ad34473ad935885b27d7eb74bec090e
3
+ metadata.gz: 60c02b77c4b06c76c050a87a0506334a469f95684c4032a0d1a4e8bc69fec387
4
+ data.tar.gz: 2464be0080e24e5c61067f6810dabd78f09ca0a7f13dafa1e049dd7b7d531233
5
5
  SHA512:
6
- metadata.gz: 53305fda5e76e31d2fae77480de9c6c66b32b3780b27b5f028fba2f95bcebe6bde23635dc6f456244533c5859d732c48c1e595a9b3ddba4a4b8a6cca679ab6df
7
- data.tar.gz: 822cd0ded5cb9508406e313abca2fdfb36899dd444e20bbc8839d28fafea2d647b4eeafc87e16e30e6918b0d3bf106ed0a46cfa4482ed6c53caa93f21a98c496
6
+ metadata.gz: 7a6e6e46fe291be06d7f9a2b91904b76170b7251861630227bbbbdf17c24a8cc3fa3b97bab83aaa98a2c46d994ddfc6707cc922e3f18b17424d254f09773c76b
7
+ data.tar.gz: f8f6fa75ff6f58562f9869122e43de7fa091925cfab4e2606011b1afa2fee0439f64ef87188ba55d62f0e98e4afc5c727b85b053aa2424cbe602cb4bdda1cc04
data/bin/miga-env ADDED
@@ -0,0 +1,6 @@
1
+ #!/usr/bin/env bash
2
+
3
+ MIGA_MOD="${MIGA_HOME:-"$HOME"}/.miga_modules"
4
+ [[ -s "$MIGA_MOD" ]] && . "$MIGA_MOD"
5
+ "$(dirname "$0")/miga" env
6
+
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 = [1.0, 5, 1].freeze
15
+ VERSION = [1.0, 5, 5].freeze
16
16
 
17
17
  ##
18
18
  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
20
20
 
21
21
  ##
22
22
  # Date of the current gem release.
23
- VERSION_DATE = Date.new(2021, 8, 26)
23
+ VERSION_DATE = Date.new(2021, 9, 14)
24
24
 
25
25
  ##
26
26
  # References of MiGA
data/scripts/miga.bash CHANGED
@@ -3,8 +3,8 @@
3
3
  ###
4
4
  # Setup environment
5
5
  set -e
6
- eval "$("$MIGA/bin/miga" env)"
7
- SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
6
+ eval "$("$MIGA/bin/miga-env")"
7
+ SCRIPT=${SCRIPT:-"$(basename "$0" .bash)"}
8
8
 
9
9
  ###
10
10
  # Ancillary functions
data/scripts/mytaxa_scan.bash CHANGED
@@ -21,7 +21,7 @@ else
21
21
  MT=$(dirname -- "$(which MyTaxa)")
22
22
  DB="$MIGA_HOME/.miga_db/AllGenomes.faa.dmnd"
23
23
  [[ -e "$DB" ]] || DB="$MT/AllGenomes.faa.dmnd"
24
- if [[ ! -e "$MT/AllGenomes.faa.dmnd" ]] ; then
24
+ if [[ ! -e "$DB" ]] ; then
25
25
  echo "Cannot locate the database: AllGenomes.faa.dmnd:" \
26
26
  "no such file or directory" >&2
27
27
  exit 1
data/utils/requirements.txt CHANGED
@@ -1,12 +1,12 @@
1
- Software Test exec Website Notes
2
- -------- --------- ------- -----
3
- Ruby ruby https://www.ruby-lang.org/ Required version: 2.3+
4
- Python python3 https://www.python.org/ Required version: 3+
1
+ Software Test exec Website Notes
2
+ -------- --------- ------- -----
3
+ Ruby ruby https://www.ruby-lang.org/ Required version: 2.3+
4
+ Python python3 https://www.python.org/ Required version: 3+
5
5
  R R http://www.r-project.org/
6
6
  SQLite3 sqlite3 https://www.sqlite.org/
7
7
  NCBI BLAST+ blastp ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
8
- DIAMOND diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.9.20+
9
- FastANI fastANI https://github.com/ParBLiSS/FastANI Required version: 1.1+
8
+ DIAMOND diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.9.20+
9
+ FastANI fastANI https://github.com/ParBLiSS/FastANI Required version: 1.1+
10
10
  HMMer 3.0+ hmmsearch http://hmmer.janelia.org/software
11
11
  Bedtools bedtools http://bedtools.readthedocs.org/en/latest/
12
12
  Prodigal prodigal http://prodigal.ornl.gov
@@ -17,6 +17,6 @@ FaQCs (reads) FaQCs https://github.com/LANL-Bioinformatics/FaQCs
17
17
  Falco (reads) falco https://github.com/smithlabcode/falco
18
18
  Seqtk (reads) seqtk https://github.com/lh3/seqtk
19
19
  Fastp (reads) fastp https://github.com/OpenGene/fastp
20
- OpenJDK (rdp) java https://adoptopenjdk.net/ Any Java VM would work
20
+ Temurin (rdp) java https://adoptium.net/ Any Java VM would work
21
21
  MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
22
22
  Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
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: 1.0.5.1
4
+ version: 1.0.5.5
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: 2021-08-26 00:00:00.000000000 Z
11
+ date: 2021-09-14 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons
@@ -107,6 +107,7 @@ files:
107
107
  - README.md
108
108
  - Rakefile
109
109
  - bin/miga
110
+ - bin/miga-env
110
111
  - lib/miga.rb
111
112
  - lib/miga/_data/aai-intax-blast.tsv.gz
112
113
  - lib/miga/_data/aai-intax-diamond.tsv.gz