iroki 0.0.27 → 0.0.28
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/.gitignore +1 -0
- data/CHANGELOG.md +5 -0
- data/bin/iroki_docker +23 -5
- data/exe/iroki +9 -1
- data/lib/iroki/color/color.rb +8 -0
- data/lib/iroki/main/main.rb +14 -1
- data/lib/iroki/utils/utils.rb +4 -0
- data/lib/iroki/version.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 7fb0a7ac745f83ec8341cbfbac699f9ac3c5f54b
|
4
|
+
data.tar.gz: decf8043b7d513ce31aef186155133d63758ddcb
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 0e823649d07424f55164ed15ecf1af65d2a72f2b7aeb1e6e57003cef2ee009b2b5c6d0b6a3a68c64cf32805499b3f99093a5a60b4842b41f9b3ed3583fa77fa7
|
7
|
+
data.tar.gz: 33f53a9b7853311080a57af7815ff5572d4f00fd2e19099b3a9bb615d14b641adbaad35b22a32fffa9fe44aebce9710e86a904b325a2044700af4d3bbcdd286e
|
data/.gitignore
CHANGED
data/CHANGELOG.md
CHANGED
data/bin/iroki_docker
CHANGED
@@ -5,17 +5,35 @@ use File::Spec;
|
|
5
5
|
my @args = ();
|
6
6
|
|
7
7
|
foreach my $arg (@ARGV) {
|
8
|
-
if ($arg =~ /^-/) {
|
8
|
+
if ($arg =~ /^-/) { # arg is a flag
|
9
9
|
push @args, $arg;
|
10
|
-
|
10
|
+
|
11
|
+
# check if next arg should expand (these are file inputs)
|
12
|
+
if ($arg eq "-c" || $arg eq "--color-map" ||
|
13
|
+
$arg eq "-i" || $arg eq "--biom" ||
|
14
|
+
$arg eq "-f" || $arg eq "--infile" ||
|
15
|
+
$arg eq "-o" || $arg eq "--outfile" ||
|
16
|
+
$arg eq "-n" || $arg eq "--name-map") {
|
17
|
+
|
18
|
+
$expand = 1;
|
19
|
+
} else {
|
20
|
+
$expand = 0;
|
21
|
+
}
|
22
|
+
} elsif ($expand) { # an arg that is a path, expand it
|
11
23
|
my $path = File::Spec->rel2abs($arg);
|
24
|
+
|
12
25
|
push @args, $path;
|
26
|
+
} else { # an arg that is not a path and not a flag
|
27
|
+
push @args, $arg;
|
13
28
|
}
|
14
29
|
}
|
15
30
|
|
16
31
|
my $img = "mooreryan/iroki";
|
17
|
-
my $
|
32
|
+
my $pull = "docker pull $img";
|
33
|
+
my $run = "docker run -v \"\$HOME:\$HOME\" $img @args";
|
18
34
|
|
19
|
-
print "\nRUNNING COMMAND: $
|
35
|
+
print "\n\n\nRUNNING COMMAND: $pull\n\n\n";
|
36
|
+
system("$pull");
|
20
37
|
|
21
|
-
|
38
|
+
print "\n\n\nRUNNING COMMAND: $run\n\n\n";
|
39
|
+
exec("$run");
|
data/exe/iroki
CHANGED
@@ -30,6 +30,8 @@ opts = Trollop.options do
|
|
30
30
|
|
31
31
|
Iroki command line program.
|
32
32
|
|
33
|
+
See https://github.com/mooreryan/iroki/wiki for the Iroki manual.
|
34
|
+
|
33
35
|
Options:
|
34
36
|
EOS
|
35
37
|
|
@@ -78,6 +80,11 @@ opts = Trollop.options do
|
|
78
80
|
opt(:outfile,
|
79
81
|
"Name of outfile",
|
80
82
|
type: :string)
|
83
|
+
|
84
|
+
opt(:default_color,
|
85
|
+
"Default color",
|
86
|
+
type: :string,
|
87
|
+
default: "black")
|
81
88
|
end
|
82
89
|
|
83
90
|
Iroki::Main.main(
|
@@ -92,5 +99,6 @@ Iroki::Main.main(
|
|
92
99
|
auto_color: opts[:auto_color],
|
93
100
|
display_auto_color_options: opts[:display_auto_color_options],
|
94
101
|
newick_f: opts[:infile],
|
95
|
-
out_f: opts[:outfile]
|
102
|
+
out_f: opts[:outfile],
|
103
|
+
default_color: opts[:default_color]
|
96
104
|
)
|
data/lib/iroki/color/color.rb
CHANGED
@@ -731,5 +731,13 @@ module Iroki
|
|
731
731
|
hex = colors[col]
|
732
732
|
%Q{[&!color="#{hex.upcase}"]}
|
733
733
|
end
|
734
|
+
|
735
|
+
def self.default_color_tag= tag_hash
|
736
|
+
@@default_color = tag_hash
|
737
|
+
end
|
738
|
+
|
739
|
+
def self.default_color_tag
|
740
|
+
@@default_color ||= nil
|
741
|
+
end
|
734
742
|
end
|
735
743
|
end
|
data/lib/iroki/main/main.rb
CHANGED
@@ -183,7 +183,8 @@ module Iroki
|
|
183
183
|
auto_color: nil,
|
184
184
|
display_auto_color_options: nil,
|
185
185
|
newick_f: nil,
|
186
|
-
out_f: nil
|
186
|
+
out_f: nil,
|
187
|
+
default_color: "black")
|
187
188
|
|
188
189
|
args = method(__method__).parameters.map { |arg| arg[1] }
|
189
190
|
AbortIf::logger.info "Args " + args.map { |arg| "#{arg} = #{eval(arg.to_s).inspect}" }.join(', ')
|
@@ -345,6 +346,18 @@ module Iroki
|
|
345
346
|
patterns = nil
|
346
347
|
end
|
347
348
|
|
349
|
+
# set default color if needed
|
350
|
+
if default_color && default_color != "black"
|
351
|
+
|
352
|
+
abort_if !default_color.hex? && !Iroki::Color::COLORS[default_color],
|
353
|
+
"--default-color must be a hex code (don't forget the '#' or a valid color. Got '#{default_color}'."
|
354
|
+
|
355
|
+
Iroki::Color::default_color_tag = { label: Iroki::Color.get_tag(default_color),
|
356
|
+
branch: Iroki::Color.get_tag(default_color), }
|
357
|
+
end
|
358
|
+
|
359
|
+
|
360
|
+
|
348
361
|
####################
|
349
362
|
# get color patterns
|
350
363
|
#################################################################
|
data/lib/iroki/utils/utils.rb
CHANGED
data/lib/iroki/version.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: iroki
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.28
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ryan Moore
|
8
8
|
autorequire:
|
9
9
|
bindir: exe
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-
|
11
|
+
date: 2016-10-13 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|