seqtrimnext 2.0.29

metadata

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+--- !ruby/object:Gem::Specification 
+name: seqtrimnext
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 2.0.29
+platform: ruby
+authors: 
+- Dario Guerrero & Almudena Bocinos
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-06-14 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: narray
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: gnuplot
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: term-ansicolor
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: xml-simple
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: scbi_blast
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: scbi_mapreduce
+  prerelease: false
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: scbi_fasta
+  prerelease: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: scbi_fastq
+  prerelease: false
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id008
+- !ruby/object:Gem::Dependency 
+  name: scbi_plot
+  prerelease: false
+  requirement: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id009
+- !ruby/object:Gem::Dependency 
+  name: scbi_math
+  prerelease: false
+  requirement: &id010 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :runtime
+  version_requirements: *id010
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id011 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.8.0
+  type: :development
+  version_requirements: *id011
+description: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce gem to be able to run in parallel and distributed environments. It is specially suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could be easyly adapted to any other situation.
+email: 
+- dariogf@gmail.com & alkoke@gmail.com
+executables: 
+- create_graphs.rb
+- extract_seqs.rb
+- extract_seqs_from_fasta.rb
+- extract_seqs_from_fastq.rb
+- fasta2fastq.rb
+- fastq2fasta.rb
+- gen_qual.rb
+- get_seq.rb
+- group_by_range.rb
+- join_ilumina_paired.rb
+- parse_amplicons.rb
+- parse_json_results.rb
+- parse_params.rb
+- resume_clusters.rb
+- resume_rejected.sh
+- reverse_paired.rb
+- seqtrimnext
+- split_fastq.rb
+- split_ilumina_paired.rb
+- split_paired.rb
+extensions: []
+
+extra_rdoc_files: 
+- lib/seqtrimnext/templates/amplicons.txt
+- lib/seqtrimnext/templates/genomics_454.txt
+- lib/seqtrimnext/templates/genomics_454_with_paired.txt
+- lib/seqtrimnext/templates/low_quality.txt
+- lib/seqtrimnext/templates/low_quality_and_low_complexity.txt
+- lib/seqtrimnext/templates/transcriptomics_454.txt
+- lib/seqtrimnext/templates/transcriptomics_plants.txt
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- bin/create_graphs.rb
+- bin/extract_seqs.rb
+- bin/extract_seqs_from_fasta.rb
+- bin/extract_seqs_from_fastq.rb
+- bin/fasta2fastq.rb
+- bin/fastq2fasta.rb
+- bin/gen_qual.rb
+- bin/get_seq.rb
+- bin/group_by_range.rb
+- bin/join_ilumina_paired.rb
+- bin/parse_amplicons.rb
+- bin/parse_json_results.rb
+- bin/parse_params.rb
+- bin/resume_clusters.rb
+- bin/resume_rejected.sh
+- bin/reverse_paired.rb
+- bin/seqtrimnext
+- bin/split_fastq.rb
+- bin/split_ilumina_paired.rb
+- bin/split_paired.rb
+- lib/seqtrimnext/actions/action_ab_adapter.rb
+- lib/seqtrimnext/actions/action_ab_far_adapter.rb
+- lib/seqtrimnext/actions/action_ab_left_adapter.rb
+- lib/seqtrimnext/actions/action_empty_insert.rb
+- lib/seqtrimnext/actions/action_ignore_repeated.rb
+- lib/seqtrimnext/actions/action_indetermination.rb
+- lib/seqtrimnext/actions/action_induced_low_complexity.rb
+- lib/seqtrimnext/actions/action_insert.rb
+- lib/seqtrimnext/actions/action_is_contaminated.rb
+- lib/seqtrimnext/actions/action_key.rb
+- lib/seqtrimnext/actions/action_left_adapter.rb
+- lib/seqtrimnext/actions/action_left_primer.rb
+- lib/seqtrimnext/actions/action_linker.rb
+- lib/seqtrimnext/actions/action_low_complexity.rb
+- lib/seqtrimnext/actions/action_low_high_size.rb
+- lib/seqtrimnext/actions/action_low_quality.rb
+- lib/seqtrimnext/actions/action_mid.rb
+- lib/seqtrimnext/actions/action_multiple_linker.rb
+- lib/seqtrimnext/actions/action_paired_reads.rb
+- lib/seqtrimnext/actions/action_poly_a.rb
+- lib/seqtrimnext/actions/action_poly_t.rb
+- lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
+- lib/seqtrimnext/actions/action_right_adapter.rb
+- lib/seqtrimnext/actions/action_right_primer.rb
+- lib/seqtrimnext/actions/action_short_insert.rb
+- lib/seqtrimnext/actions/action_unexpected_poly_t.rb
+- lib/seqtrimnext/actions/action_unexpected_vector.rb
+- lib/seqtrimnext/actions/action_vectors.rb
+- lib/seqtrimnext/actions/seqtrim_action.rb
+- lib/seqtrimnext/classes/action_manager.rb
+- lib/seqtrimnext/classes/em_classes/seqtrim_work_manager.rb
+- lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb
+- lib/seqtrimnext/classes/extract_stats.rb
+- lib/seqtrimnext/classes/gnu_plot_graph.rb
+- lib/seqtrimnext/classes/graph_stats.rb
+- lib/seqtrimnext/classes/install_database.rb
+- lib/seqtrimnext/classes/install_requirements.rb
+- lib/seqtrimnext/classes/list_db.rb
+- lib/seqtrimnext/classes/make_blast_db.rb
+- lib/seqtrimnext/classes/one_blast.rb
+- lib/seqtrimnext/classes/params.rb
+- lib/seqtrimnext/classes/piro.rb
+- lib/seqtrimnext/classes/plugin_manager.rb
+- lib/seqtrimnext/classes/scan_for_restr_site.rb
+- lib/seqtrimnext/classes/scbi_stats.rb
+- lib/seqtrimnext/classes/seqtrim.rb
+- lib/seqtrimnext/classes/sequence.rb
+- lib/seqtrimnext/classes/sequence_group.rb
+- lib/seqtrimnext/classes/sequence_with_action.rb
+- lib/seqtrimnext/plugins/plugin.rb
+- lib/seqtrimnext/plugins/plugin_ab_adapters.rb
+- lib/seqtrimnext/plugins/plugin_adapters.rb
+- lib/seqtrimnext/plugins/plugin_amplicons.rb
+- lib/seqtrimnext/plugins/plugin_contaminants.rb
+- lib/seqtrimnext/plugins/plugin_extract_inserts.rb
+- lib/seqtrimnext/plugins/plugin_find_poly_at.rb
+- lib/seqtrimnext/plugins/plugin_ignore_repeated.rb
+- lib/seqtrimnext/plugins/plugin_indeterminations.rb
+- lib/seqtrimnext/plugins/plugin_key.rb
+- lib/seqtrimnext/plugins/plugin_linker.rb
+- lib/seqtrimnext/plugins/plugin_low_complexity.rb
+- lib/seqtrimnext/plugins/plugin_low_high_size.rb
+- lib/seqtrimnext/plugins/plugin_low_quality.rb
+- lib/seqtrimnext/plugins/plugin_mids.rb
+- lib/seqtrimnext/plugins/plugin_rem_adit_artifacts.rb
+- lib/seqtrimnext/plugins/plugin_short_insert.rb
+- lib/seqtrimnext/plugins/plugin_vectors.rb
+- lib/seqtrimnext/templates/amplicons.txt
+- lib/seqtrimnext/templates/genomics_454.txt
+- lib/seqtrimnext/templates/genomics_454_with_paired.txt
+- lib/seqtrimnext/templates/low_quality.txt
+- lib/seqtrimnext/templates/low_quality_and_low_complexity.txt
+- lib/seqtrimnext/templates/transcriptomics_454.txt
+- lib/seqtrimnext/templates/transcriptomics_plants.txt
+- lib/seqtrimnext/utils/extract_samples.rb
+- lib/seqtrimnext/utils/fasta2xml.rb
+- lib/seqtrimnext/utils/global_match.rb
+- lib/seqtrimnext/utils/hash_stats.rb
+- lib/seqtrimnext/utils/json_utils.rb
+- lib/seqtrimnext/utils/load_fasta_names_in_hash.rb
+- lib/seqtrimnext/utils/load_qual_in_hash.rb
+- lib/seqtrimnext/utils/recover_mid.rb
+- lib/seqtrimnext/utils/string_utils.rb
+- lib/seqtrimnext.rb
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+- Rakefile
+- README.rdoc
+- script/console
+- script/destroy
+- script/generate
+- test/test_helper.rb
+- test/test_seqtrimnext.rb
+homepage: http://www.scbi.uma.es/downloads
+licenses: []
+
+post_install_message: PostInstall.txt
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: seqtrimnext
+rubygems_version: 1.7.2
+signing_key: 
+specification_version: 3
+summary: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data
+test_files: 
+- test/test_helper.rb
+- test/test_seqtrimnext.rb