ribopip.gemspec
## This is the rakegem gemspec template. Make sure you read and understand
## all of the comments. Some sections require modification, and others can
## be deleted if you don't need them. Once you understand the contents of
## this file, feel free to delete any comments that begin with two hash marks.
## You can find comprehensive Gem::Specification documentation, at
## http://docs.rubygems.org/read/chapter/20
Gem::Specification.new do |s|
s.specification_version = 2 if s.respond_to? :specification_version=
s.required_rubygems_version = Gem::Requirement.new('>= 0') if s.respond_to? :required_rubygems_version=
s.rubygems_version = '1.3.5'
## Leave these as is they will be modified for you by the rake gemspec task.
## If your rubyforge_project name is different, then edit it and comment out
## the sub! line in the Rakefile
s.name = 'ribopip'
s.version = '0.1.0'
s.date = '2016-04-29'
s.rubyforge_project = 'ribopip'
## Make sure your summary is short. The description may be as long
## as you like.
s.summary = 'An alignment and analysis pipeline for Ribosome Profiling' \
'Data.'
s.description = 'Long description. Maybe copied from the README.'
## List the primary authors. If there are a bunch of authors, it's probably
## better to set the email to an email list or something. If you don't have
## a custom homepage, consider using your GitHub URL or the like.
s.authors = ['Stefan Dang']
s.email = 'stefan@man-dangt.de'
s.homepage = 'http://github.com/stepf'
## This gets added to the $LOAD_PATH so that 'lib/NAME.rb' can be required as
## require 'NAME.rb' or'/lib/NAME/file.rb' can be as require 'NAME/file.rb'
s.require_paths = %w(lib)
## This sections is only necessary if you have C extensions.
# s.require_paths << 'ext'
# s.extensions = %w(ext/fastq_bucketize/extconf.rb)
## If your gem includes any executables, list them here.
# s.executables = ["name"]
## Specify any RDoc options here. You'll want to add your README and
## LICENSE files to the extra_rdoc_files list.
s.rdoc_options = ['--charset=UTF-8']
#s.extra_rdoc_files = %w[README LICENSE]
## List your runtime dependencies here. Runtime dependencies are those
## that are needed for an end user to actually USE your code.
s.add_dependency('thor', ['>= 0.19.1'])
## List your development dependencies here. Development dependencies are
## those that are only needed during development
# s.add_development_dependency('DEVDEPNAME', [">= 1.1.0", "< 2.0.0"])
s.add_development_dependency('rdoc', ['>= 3.2.3'])
s.add_development_dependency('rspec', ['>= 3.5.0'])
s.add_development_dependency('simplecov', ['>= 0.12.0'])
## Leave this section as-is. It will be automatically generated from the
## contents of your Git repository via the gemspec task. DO NOT REMOVE
## THE MANIFEST COMMENTS, they are used as delimiters by the task.
# = MANIFEST =
s.files = %w[
Gemfile
Rakefile
bin/ribopip
lib/ribopip.rb
lib/ribopip/array_writer.rb
lib/ribopip/binary_checker.rb
lib/ribopip/cli.rb
lib/ribopip/counts.rb
lib/ribopip/deseq.rb
lib/ribopip/expression_analysis.rb
lib/ribopip/feature_counts.rb
lib/ribopip/filenames.rb
lib/ribopip/gene_id_2_name.rb
lib/ribopip/metrics.rb
lib/ribopip/pipeline.rb
ribopip.gemspec
scripts/join_counts.rb
scripts/run_deseq1.R
scripts/run_deseq2.R
spec/array_writer_spec.rb
spec/binary_checker_spec.rb
spec/counts_spec.rb
spec/expression_analysis_spec.rb
spec/filenames_spec.rb
spec/gene_id_2_name_spec.rb
spec/metrics_spec.rb
spec/pipeline_spec.rb
spec/ribopip_spec.rb
spec/spec_helper.rb
spec/testdata/SRR315601_625.fastq
spec/testdata/array_writer/SRR315601_625.counts.tsv
spec/testdata/array_writer/SRR315601_625.counts.xml
spec/testdata/array_writer/expected_read_counts.tsv
spec/testdata/array_writer/expected_read_counts.xml
spec/testdata/counts/align_summary.txt
spec/testdata/counts/uni_mapped_0err.bam
spec/testdata/expression_analysis/d1_vs_d2.counts
spec/testdata/expression_analysis/d1_vs_d2.deseq.counts.tsv
spec/testdata/expression_analysis/d1_vs_d2.deseq1.all.csv
spec/testdata/expression_analysis/d1_vs_d2.deseq1.all.ft.csv
spec/testdata/expression_analysis/d1_vs_d2.deseq1.log
spec/testdata/expression_analysis/d1_vs_d2.deseq1.padj.ft.csv
spec/testdata/expression_analysis/d1_vs_d2.rdiff.results.tsv
spec/testdata/expression_analysis/dummy1_rep1.txt
spec/testdata/expression_analysis/dummy1_rep2.txt
spec/testdata/expression_analysis/dummy2_rep1.txt
spec/testdata/expression_analysis/dummy2_rep2.txt
spec/testdata/expression_analysis/expected.all.ft.csv
spec/testdata/expression_analysis/expected.all.ft.norm.csv
spec/testdata/expression_analysis/expected.rdiff.outline.csv
spec/testdata/expression_analysis/expected.rdiff.results.padj.tsv
spec/testdata/expression_analysis/expected_d1_vs_d2.counts
spec/testdata/expression_analysis/expected_names.xml
spec/testdata/expression_analysis/mrna.deseq1.all.ft.csv
spec/testdata/expression_analysis/mrna.deseq1.padj.ft.csv
spec/testdata/expression_analysis/names.csv
spec/testdata/expression_analysis/names.xml
spec/testdata/gene_id_2_name/d1_vs_d2.deseq1.all.ft.csv
spec/testdata/gene_id_2_name/d1_vs_d2.deseq1.names.csv
spec/testdata/gene_id_2_name/expected.names.csv
spec/testdata/ref/expected.name_index
spec/testdata/ref/mini.GRCm38.80.gtf
spec/testdata/statistics/SRR315601_625.fastq.gt_seqstat
spec/testdata/statistics/expected.gt_seqstat
]
# = MANIFEST =
## Test files will be grabbed from the file list. Make sure the path glob
## matches what you actually use.
s.test_files = s.files.select { |path| path =~ /^test\/test_.*\.rb/ }
end