ulla 0.9.7 → 0.9.8
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- data/History.txt +4 -0
- data/Manifest.txt +0 -1
- data/README.rdoc +8 -7
- data/Rakefile +14 -21
- data/lib/ulla.rb +1 -1
- data/lib/ulla/cli.rb +4 -4
- data/ulla.gemspec +9 -10
- data/website/index.html +1 -1
- metadata +4 -16
- data/.autotest +0 -5
data/History.txt
CHANGED
data/Manifest.txt
CHANGED
data/README.rdoc
CHANGED
@@ -49,7 +49,10 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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49
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--classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
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--outfile (-o) FILE: output filename (default 'allmat.dat')
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--weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
|
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-
--noweight: calculate substitution
|
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+
--noweight: calculate substitution counts with no weights
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+
--environment (-e) INTEGER:
|
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+
0 for considering only substituted amino acids' environments (default)
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+
1 for considering both substituted and substituting amino acids' environments
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--smooth (-s) INTEGER:
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0 for partial smoothing (default)
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1 for full smoothing
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@@ -60,14 +63,14 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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1 for both structure and sequence
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2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
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--output INTEGER:
|
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-
0 for raw
|
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+
0 for raw counts (no smoothing performed)
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1 for probabilities
|
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-
2 for log
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+
2 for log-odds (default)
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--noroundoff: do not round off log odds ratio
|
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-
--scale INTEGER: log
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+
--scale INTEGER: log-odds matrices in 1/n bit units (default 3)
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--sigma DOUBLE: change the sigma value for smoothing (default 5.0)
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--autosigma: automatically adjust the sigma value for smoothing
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-
--add DOUBLE: add this value to raw
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+
--add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 0)
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--pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
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--pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
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--heatmap INTEGER:
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@@ -234,8 +237,6 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
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== TODO
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-
* Substitution table generation considering both the source and the target environmental classes
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-
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== Repository
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You can download a pre-built RubyGems package from
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data/Rakefile
CHANGED
@@ -1,32 +1,25 @@
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1
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-
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2
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-
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1
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+
require 'rubygems'
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+
gem 'hoe', '>= 2.1.0'
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+
require 'hoe'
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+
require 'fileutils'
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+
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Hoe.plugin :newgem
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# Hoe.plugin :website
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8
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+
# Hoe.plugin :cucumberfeatures
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3
9
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# Generate all the Rake tasks
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# Run 'rake -T' to see list of generated tasks (from gem root directory)
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-
$hoe = Hoe.
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-
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-
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9
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-
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-
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11
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-
p.extra_deps = [
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+
$hoe = Hoe.spec 'ulla' do
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+
self.developer 'Semin Lee', 'seminlee@gmail.com'
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+
self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
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+
self.rubyforge_name = self.name # TODO this is default value
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+
self.extra_deps = [
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['narray', '>= 0.5.9.5'],
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['bio', '>= 1.2.1'],
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['facets', '>= 2.4.5'],
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['rmagick', '>= 2.9.1'],
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]
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-
|
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-
p.extra_dev_deps = [
|
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-
['newgem', ">= #{::Newgem::VERSION}"]
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-
]
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-
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-
p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
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-
path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
|
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-
p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
|
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-
p.rsync_args = '-av --delete --ignore-errors'
|
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end
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-
require 'newgem/tasks'
|
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+
require 'newgem/tasks'
|
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Dir['tasks/**/*.rake'].each { |t| load t }
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-
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-
# TODO - want other tests/tasks run by default? Add them to the list
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-
# task :default => [:spec, :features]
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data/lib/ulla.rb
CHANGED
data/lib/ulla/cli.rb
CHANGED
@@ -384,7 +384,7 @@ Options:
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# if --cys option 2, then we don't care about 'J' (for both Cystine and Cystine)
|
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if $cys == 2
|
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-
$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J')
|
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+
$amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J').split('')
|
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end
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# create an EnvironmentFeatureArray object for storing all environment
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@@ -709,11 +709,11 @@ Options:
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env_label2 = $environment == 1 ? aa2 + '-' + aa1[1..-1] : env_labels[id2][pos]
|
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if $cst_features.empty?
|
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-
$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
|
713
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-
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
|
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+
$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
|
713
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+
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
|
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elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
|
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715
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$env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
|
716
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-
$env_classes[env_label2].increase_residue_count(aa1[
|
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+
$env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
|
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else
|
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$logger.debug "Skipped #{id1}-#{pos}-#{aa1[0].chr} and #{id2}-#{pos}-#{aa2[0].chr} having different symbols for constrained environment features each other."
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next
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data/ulla.gemspec
CHANGED
@@ -2,44 +2,43 @@
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2
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Gem::Specification.new do |s|
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s.name = %q{ulla}
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-
s.version = "0.9.
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5
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+
s.version = "0.9.7"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Semin Lee"]
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-
s.date = %q{2009-
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+
s.date = %q{2009-06-11}
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s.default_executable = %q{ulla}
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s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
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s.email = ["seminlee@gmail.com"]
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s.executables = ["ulla"]
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s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
|
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-
s.files = ["
|
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-
s.has_rdoc = true
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15
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+
s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
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s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
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s.post_install_message = %q{PostInstall.txt}
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s.rdoc_options = ["--main", "README.rdoc"]
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s.require_paths = ["lib"]
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s.rubyforge_project = %q{ulla}
|
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-
s.rubygems_version = %q{1.3.
|
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+
s.rubygems_version = %q{1.3.4}
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s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
|
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-
s.test_files = ["test/
|
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+
s.test_files = ["test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb"]
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25
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if s.respond_to? :specification_version then
|
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current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
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-
s.specification_version =
|
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+
s.specification_version = 3
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if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
|
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s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
|
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s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
|
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s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
|
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s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
|
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-
s.add_development_dependency(%q<newgem>, [">= 1.
|
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+
s.add_development_dependency(%q<newgem>, [">= 1.4.1"])
|
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s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
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else
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s.add_dependency(%q<narray>, [">= 0.5.9.5"])
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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-
s.add_dependency(%q<newgem>, [">= 1.
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+
s.add_dependency(%q<newgem>, [">= 1.4.1"])
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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end
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else
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@@ -47,7 +46,7 @@ Gem::Specification.new do |s|
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s.add_dependency(%q<bio>, [">= 1.2.1"])
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s.add_dependency(%q<facets>, [">= 2.4.5"])
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s.add_dependency(%q<rmagick>, [">= 2.9.1"])
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-
s.add_dependency(%q<newgem>, [">= 1.
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+
s.add_dependency(%q<newgem>, [">= 1.4.1"])
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s.add_dependency(%q<hoe>, [">= 1.8.0"])
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end
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end
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data/website/index.html
CHANGED
@@ -4,7 +4,7 @@
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<head>
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<meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
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<title>
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-
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+
Ulla: a program for calculating environment-specific substitution tables
|
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</title>
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</head>
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<body>
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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--- !ruby/object:Gem::Specification
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name: ulla
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version: !ruby/object:Gem::Version
|
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-
version: 0.9.
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+
version: 0.9.8
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platform: ruby
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authors:
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- Semin Lee
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@@ -9,7 +9,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2009-
|
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+
date: 2009-07-21 00:00:00 +01:00
|
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default_executable:
|
14
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dependencies:
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- !ruby/object:Gem::Dependency
|
@@ -52,16 +52,6 @@ dependencies:
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- !ruby/object:Gem::Version
|
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version: 2.9.1
|
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version:
|
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-
- !ruby/object:Gem::Dependency
|
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-
name: newgem
|
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|
-
type: :development
|
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version_requirement:
|
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-
version_requirements: !ruby/object:Gem::Requirement
|
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-
requirements:
|
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-
- - ">="
|
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|
-
- !ruby/object:Gem::Version
|
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|
-
version: 1.4.1
|
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|
-
version:
|
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|
- !ruby/object:Gem::Dependency
|
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name: hoe
|
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type: :development
|
@@ -70,7 +60,7 @@ dependencies:
|
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requirements:
|
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- - ">="
|
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- !ruby/object:Gem::Version
|
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|
-
version:
|
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+
version: 2.3.2
|
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version:
|
75
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|
description: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
|
76
66
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email:
|
@@ -83,10 +73,8 @@ extra_rdoc_files:
|
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- History.txt
|
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- Manifest.txt
|
85
75
|
- PostInstall.txt
|
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-
- README.rdoc
|
87
76
|
- website/index.txt
|
88
77
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files:
|
89
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-
- .autotest
|
90
78
|
- History.txt
|
91
79
|
- Manifest.txt
|
92
80
|
- PostInstall.txt
|
@@ -150,7 +138,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
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138
|
requirements: []
|
151
139
|
|
152
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rubyforge_project: ulla
|
153
|
-
rubygems_version: 1.3.
|
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|
+
rubygems_version: 1.3.4
|
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signing_key:
|
155
143
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specification_version: 3
|
156
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|
summary: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
|