RubyGems - miga-base - Versions diffs - 0.2.0.6 - Mend

miga-base 0.2.0.6

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Files changed (52) hide show

checksums.yaml +7 -0
data/README.md +351 -0
data/actions/add_result +61 -0
data/actions/add_taxonomy +86 -0
data/actions/create_dataset +62 -0
data/actions/create_project +70 -0
data/actions/daemon +69 -0
data/actions/download_dataset +77 -0
data/actions/find_datasets +63 -0
data/actions/import_datasets +86 -0
data/actions/index_taxonomy +71 -0
data/actions/list_datasets +83 -0
data/actions/list_files +67 -0
data/actions/unlink_dataset +52 -0
data/bin/miga +48 -0
data/lib/miga/daemon.rb +178 -0
data/lib/miga/dataset.rb +286 -0
data/lib/miga/gui.rb +289 -0
data/lib/miga/metadata.rb +74 -0
data/lib/miga/project.rb +268 -0
data/lib/miga/remote_dataset.rb +154 -0
data/lib/miga/result.rb +102 -0
data/lib/miga/tax_index.rb +70 -0
data/lib/miga/taxonomy.rb +107 -0
data/lib/miga.rb +83 -0
data/scripts/_distances_noref_nomulti.bash +86 -0
data/scripts/_distances_ref_nomulti.bash +105 -0
data/scripts/aai_distances.bash +40 -0
data/scripts/ani_distances.bash +39 -0
data/scripts/assembly.bash +38 -0
data/scripts/cds.bash +45 -0
data/scripts/clade_finding.bash +27 -0
data/scripts/distances.bash +30 -0
data/scripts/essential_genes.bash +29 -0
data/scripts/haai_distances.bash +39 -0
data/scripts/init.bash +211 -0
data/scripts/miga.bash +12 -0
data/scripts/mytaxa.bash +93 -0
data/scripts/mytaxa_scan.bash +85 -0
data/scripts/ogs.bash +36 -0
data/scripts/read_quality.bash +37 -0
data/scripts/ssu.bash +35 -0
data/scripts/subclades.bash +26 -0
data/scripts/trimmed_fasta.bash +47 -0
data/scripts/trimmed_reads.bash +57 -0
data/utils/adapters.fa +302 -0
data/utils/mytaxa_scan.R +89 -0
data/utils/mytaxa_scan.rb +58 -0
data/utils/requirements.txt +19 -0
data/utils/subclades-compile.rb +48 -0
data/utils/subclades.R +171 -0
metadata +185 -0

metadata ADDED Viewed

@@ -0,0 +1,185 @@
+--- !ruby/object:Gem::Specification
+name: miga-base
+version: !ruby/object:Gem::Version
+  version: 0.2.0.6
+platform: ruby
+authors:
+- Luis M. Rodriguez-R
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2015-12-07 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: sqlite3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: daemons
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.2'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.2'
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Microbial Genomes Atlas
+email: lmrodriguezr@gmail.com
+executables:
+- miga
+extensions: []
+extra_rdoc_files:
+- README.md
+files:
+- lib/miga.rb
+- lib/miga/daemon.rb
+- lib/miga/dataset.rb
+- lib/miga/gui.rb
+- lib/miga/metadata.rb
+- lib/miga/project.rb
+- lib/miga/remote_dataset.rb
+- lib/miga/result.rb
+- lib/miga/tax_index.rb
+- lib/miga/taxonomy.rb
+- scripts/_distances_noref_nomulti.bash
+- scripts/_distances_ref_nomulti.bash
+- scripts/aai_distances.bash
+- scripts/ani_distances.bash
+- scripts/assembly.bash
+- scripts/cds.bash
+- scripts/clade_finding.bash
+- scripts/distances.bash
+- scripts/essential_genes.bash
+- scripts/haai_distances.bash
+- scripts/init.bash
+- scripts/miga.bash
+- scripts/mytaxa.bash
+- scripts/mytaxa_scan.bash
+- scripts/ogs.bash
+- scripts/read_quality.bash
+- scripts/ssu.bash
+- scripts/subclades.bash
+- scripts/trimmed_fasta.bash
+- scripts/trimmed_reads.bash
+- utils/adapters.fa
+- utils/mytaxa_scan.R
+- utils/mytaxa_scan.rb
+- utils/requirements.txt
+- utils/subclades-compile.rb
+- utils/subclades.R
+- bin/miga
+- actions/add_result
+- actions/add_taxonomy
+- actions/create_dataset
+- actions/create_project
+- actions/daemon
+- actions/download_dataset
+- actions/find_datasets
+- actions/import_datasets
+- actions/index_taxonomy
+- actions/list_datasets
+- actions/list_files
+- actions/unlink_dataset
+- README.md
+homepage: http://enve-omics.ce.gatech.edu/miga
+licenses:
+- artistic 2.0
+metadata: {}
+post_install_message:
+rdoc_options:
+- lib
+- README.md
+- --main
+- README.md
+- --title
+- MiGA
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ~>
+    - !ruby/object:Gem::Version
+      version: '2.0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.0.14
+signing_key:
+specification_version: 4
+summary: MiGA
+test_files: []