coutinho_assembly 0.1.0 → 0.2.0
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/README.md +5 -1
- data/exe/coutinho_assembly +10 -0
- data/lib/coutinho_assembly/version.rb +1 -1
- data/lib/coutinho_assembly.rb +2 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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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: 9cef186eff0a2e1a788f727e0c4f78aac4399a9a
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4
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+
data.tar.gz: 39ad07d3c8328f142070dfd24f5ff48a2b9cd8cc
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 40821919c72befb6fb038034f4e8734cdfacfa155f2e0cb20ee1c4ec77228d4b914d6b16f66e520e736d852636a40d972709d297aba1290acfd74b0c2f9f5dae
|
7
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+
data.tar.gz: 52e8f82160edb9b20eb8db390c3a4ee833d568728457fe57ea3b04cd4e51c5f80079fd6c7c1fcc400e2bdd1ea4ff4f3867e9470ea7cc4d2c1dcb8ec514c39c70
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data/Gemfile.lock
CHANGED
data/README.md
CHANGED
data/exe/coutinho_assembly
CHANGED
@@ -77,6 +77,11 @@ opts = Optimist.options do
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77
77
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"Max no. retries before giving up on a pipeline step.",
|
78
78
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default: 10)
|
79
79
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|
80
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+
# Megahit options
|
81
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+
opt(:megahit_presets,
|
82
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+
"meta-sensitive, meta-large, or fast",
|
83
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+
default: "meta-sensitive")
|
84
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+
|
80
85
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# External programs I depend on
|
81
86
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opt(:megahit_binary,
|
82
87
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"Path to megahit binary",
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@@ -138,6 +143,11 @@ Rya::AbortIf.abort_if num_threads < 1,
|
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138
143
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Rya::AbortIf.abort_if max_attempts < 1,
|
139
144
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"--max-attempts must be at least 1"
|
140
145
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|
146
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+
GOOD_PRESETS = %w[meta-sensitive meta-large fast]
|
147
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+
megahit_preset = opts[:megahit_presets]
|
148
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+
Rya::AbortIf.abort_unless megahit_preset.nil? || GOOD_PRESETS.include?(megahit_preset),
|
149
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+
"--megahit-presets must be one of #{GOOD_PRESETS.join(", ")}. Got #{megahit_preset}"
|
150
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+
|
141
151
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megahit_binary = opts[:megahit_binary]
|
142
152
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sample_seqs_binary = opts[:sample_seqs_binary]
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143
153
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zip_binary = opts[:zip_binary]
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data/lib/coutinho_assembly.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: coutinho_assembly
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3
3
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version: !ruby/object:Gem::Version
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4
|
-
version: 0.
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4
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+
version: 0.2.0
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5
5
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platform: ruby
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6
6
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authors:
|
7
7
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- Ryan Moore
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8
8
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autorequire:
|
9
9
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bindir: exe
|
10
10
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cert_chain: []
|
11
|
-
date: 2019-
|
11
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+
date: 2019-04-15 00:00:00.000000000 Z
|
12
12
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dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
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name: bundler
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