--- !ruby/object:Gem::Specification
name: seqtrimnext
version: !ruby/object:Gem::Version
  version: 2.0.68
platform: ruby
authors:
- Dario Guerrero
- Almudena Bocinos
autorequire: 
bindir: bin
cert_chain: []
date: 2016-12-14 00:00:00.000000000 Z
dependencies:
- !ruby/object:Gem::Dependency
  name: bundler
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.7'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '1.7'
- !ruby/object:Gem::Dependency
  name: rake
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '10.0'
  type: :development
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - "~>"
      - !ruby/object:Gem::Version
        version: '10.0'
- !ruby/object:Gem::Dependency
  name: narray
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: gnuplot
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: '0'
- !ruby/object:Gem::Dependency
  name: term-ansicolor
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.5
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.5
- !ruby/object:Gem::Dependency
  name: xml-simple
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.12
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 1.0.12
- !ruby/object:Gem::Dependency
  name: scbi_blast
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.34
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.34
- !ruby/object:Gem::Dependency
  name: scbi_mapreduce
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.38
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.38
- !ruby/object:Gem::Dependency
  name: scbi_fasta
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.1.7
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.1.7
- !ruby/object:Gem::Dependency
  name: scbi_fastq
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.18
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.18
- !ruby/object:Gem::Dependency
  name: scbi_plot
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.6
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.6
- !ruby/object:Gem::Dependency
  name: scbi_math
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.1
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.1
- !ruby/object:Gem::Dependency
  name: scbi_headers
  requirement: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.2
  type: :runtime
  prerelease: false
  version_requirements: !ruby/object:Gem::Requirement
    requirements:
    - - ">="
      - !ruby/object:Gem::Version
        version: 0.0.2
description: Seqtrimnext is a plugin based system to preprocess and clean sequences
  from multiple NGS sequencing platforms
email:
- dariogf@gmail.com
- |-
  alkoke@gmail.com
  t
executables:
- create_graphs.rb
- extract_seqs.rb
- extract_seqs_from_fasta.rb
- extract_seqs_from_fastq.rb
- fasta2fastq.rb
- fastq2fasta.rb
- filter_database.rb
- gen_qual.rb
- get_seq.rb
- group_by_range.rb
- join_big_illumina_paired.sh
- join_ilumina_paired.rb
- parse_amplicons.rb
- parse_json_results.rb
- parse_params.rb
- resume_clusters.rb
- resume_execution_times.rb
- resume_rejected.rb
- resume_stn_contaminants.rb
- resume_stn_stats.rb
- reverse_paired.rb
- seqtrimnext
- split_fasta.rb
- split_fastq.rb
- split_ilumina_paired.rb
- split_paired.rb
extensions: []
extra_rdoc_files: []
files:
- ".gitignore"
- Gemfile
- LICENSE.txt
- README.md
- Rakefile
- 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/filter_database.rb
- bin/gen_qual.rb
- bin/get_seq.rb
- bin/group_by_range.rb
- bin/join_big_illumina_paired.sh
- bin/join_ilumina_paired.rb
- bin/parse_amplicons.rb
- bin/parse_json_results.rb
- bin/parse_params.rb
- bin/resume_clusters.rb
- bin/resume_execution_times.rb
- bin/resume_rejected.rb
- bin/resume_stn_contaminants.rb
- bin/resume_stn_stats.rb
- bin/reverse_paired.rb
- bin/seqtrimnext
- bin/split_fasta.rb
- bin/split_fastq.rb
- bin/split_ilumina_paired.rb
- bin/split_paired.rb
- lib/seqtrimnext.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_middle_adapter.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_sanger_left_adapter.rb
- lib/seqtrimnext/actions/action_sanger_right_adapter.rb
- lib/seqtrimnext/actions/action_short_insert.rb
- lib/seqtrimnext/actions/action_trim.rb
- lib/seqtrimnext/actions/action_unexpected_poly_t.rb
- lib/seqtrimnext/actions/action_unexpected_vector.rb
- lib/seqtrimnext/actions/action_user_contaminant.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/.DS_Store
- 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_sanger_adapters.rb
- lib/seqtrimnext/plugins/plugin_short_insert.rb
- lib/seqtrimnext/plugins/plugin_size_trim.rb
- lib/seqtrimnext/plugins/plugin_user_contaminants.rb
- lib/seqtrimnext/plugins/plugin_vectors.rb
- lib/seqtrimnext/plugins_old/.DS_Store
- lib/seqtrimnext/plugins_old/plugin_adapters_old.rb
- lib/seqtrimnext/plugins_old/plugin_low_quality_old.rb
- lib/seqtrimnext/plugins_old/plugin_rem_adit_artifacts.rb
- lib/seqtrimnext/templates/amplicons.txt
- lib/seqtrimnext/templates/genomics_454.txt
- lib/seqtrimnext/templates/genomics_454_with_paired.txt
- lib/seqtrimnext/templates/genomics_short_reads.txt
- lib/seqtrimnext/templates/genomics_short_reads_2.txt
- lib/seqtrimnext/templates/only_quality.txt
- lib/seqtrimnext/templates/sanger.txt
- lib/seqtrimnext/templates/transcriptomics_454.txt
- lib/seqtrimnext/templates/transcriptomics_454_plants.txt
- lib/seqtrimnext/templates/transcriptomics_short_reads.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/version.rb
- seqtrimnext.gemspec
homepage: ''
licenses:
- MIT
metadata: {}
post_install_message: 
rdoc_options: []
require_paths:
- lib
required_ruby_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
required_rubygems_version: !ruby/object:Gem::Requirement
  requirements:
  - - ">="
    - !ruby/object:Gem::Version
      version: '0'
requirements: []
rubyforge_project: 
rubygems_version: 2.4.8
signing_key: 
specification_version: 4
summary: Sequences preprocessing and cleaning software
test_files: []