--- !ruby/object:Gem::Specification 
name: seqtrimnext
version: !ruby/object:Gem::Version 
  prerelease: 
  version: 2.0.51
platform: ruby
authors: 
- Dario Guerrero & Almudena Bocinos
autorequire: 
bindir: bin
cert_chain: []

date: 2012-06-20 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: 1.0.5
  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: 1.0.12
  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: 0.0.34
  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: 0.0.38
  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: 0.1.7
  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: 0.0.16
  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: 0.0.6
  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: 0.0.1
  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
- 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_rejected.rb
- reverse_paired.rb
- seqtrimnext
- split_fastq.rb
- split_ilumina_paired.rb
- split_paired.rb
extensions: []

extra_rdoc_files: 
- History.txt
- 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/transcriptomics_454.txt
- lib/seqtrimnext/templates/transcriptomics_short_reads.txt
- lib/seqtrimnext/templates/transcriptomics_plants.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/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_rejected.rb
- bin/reverse_paired.rb
- bin/seqtrimnext
- bin/split_fastq.rb
- bin/split_ilumina_paired.rb
- bin/split_paired.rb
- History.txt
- 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_classify.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_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_adapters_old.rb
- lib/seqtrimnext/plugins/plugin_amplicons.rb
- lib/seqtrimnext/plugins/plugin_contaminants.rb
- lib/seqtrimnext/plugins/plugin_user_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/genomics_short_reads.txt
- lib/seqtrimnext/templates/genomics_short_reads_2.txt
- lib/seqtrimnext/templates/transcriptomics_454.txt
- lib/seqtrimnext/templates/transcriptomics_short_reads.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
- 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: 1.8.24
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