sequence_logo 1.3.0 → 1.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 32b477a05d970c0504ddd097aba85fae5f2f99da68fcd391fcfae2292742eb6c
-  data.tar.gz: c35413b1a0b77c12ea272a99edfc98a17bae66a3b9b9cee4c5db51995016e070
+  metadata.gz: dc12b7725ab623ff5dee66a5925bbaf2a03a0cc3297e8c3e5f5a97b6c60a390e
+  data.tar.gz: aadd4b89207c6caf3d8ec80af8274d44e380c0996fb7c6894dd4f01ddecaab82
 SHA512:
-  metadata.gz: 7ca7a02cbecc38cd15b7c622786e0eb0eeb06840133a941ac340cc07f2bc7da0981ea1da4e082e675a7541da2eea2e6cd7d303ca10b8d16327d85884c5a675e4
-  data.tar.gz: 5835d5a6e720753e2555cf0a8dc13a9752f610506bae4c41e1bf582cd75602b8f7940963ffc29b10f1b152e4b5097953c334e8289f5892a3723ddc518d48afb8
+  metadata.gz: b3d6d67a23eca984f0113994cc7cce8a6565ad2dfa5091aa3f4ceeb29adfa8cba41f5ca7c750bb6164d112d517e7779ba319de208e9c19c5138509904defef42
+  data.tar.gz: 4521b699696fada1861cbd0e568a7ee269e43ed0aec6a545f3b2f4d1c3b6398a6aca7998ac0a3c19dae575e1a36eec2ff4aa20b0d91d636253ea75273c5208a7

data/docker/Dockerfile-rmagick-alpine

@@ -0,0 +1,14 @@
+FROM ruby:alpine
+RUN apk add --virtual .builddeps --update  alpine-sdk curl gzip tar && \
+    curl -o ImageMagick-6.9.10-14.tar.gz "http://mirror.checkdomain.de/imagemagick/ImageMagick-6.9.10-14.tar.gz" && \
+    tar -zxf ImageMagick-6.9.10-14.tar.gz && \
+    apk add --update libgcc libgomp libjpeg-turbo-dev libpng-dev && \
+    cd ImageMagick-6.9.10-14 && \
+    ./configure && \
+    make && \
+    make install && \
+    gem install rmagick --no-document && \
+    apk del .builddeps && \
+    cd / && \
+    rm -rf ImageMagick-6.9.10-14.tar.gz ImageMagick-6.9.10-14 && \
+    rm -rf /var/cache/apk/*

data/docker/Dockerfile-rmagick-slim

@@ -0,0 +1,8 @@
+FROM ruby:slim
+RUN apt-get update && \
+    apt-get install -y ruby build-essential imagemagick libmagickcore-dev libmagickwand-dev pkg-config && \
+    gem install rmagick && \
+    apt-get purge -y build-essential libmagickcore-dev libmagickwand-dev pkg-config && \
+    apt-get autoremove -y && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*

data/docker/Dockerfile-sequence_logo

@@ -0,0 +1,6 @@
+FROM vorontsovie/rmagick:alpine
+RUN gem install sequence_logo
+WORKDIR /data
+ENTRYPOINT ["sequence_logo"]
+CMD ["--help"]
+# docker run --rm --mount type=bind,src=$(pwd),dst=/data sequence_logo motif.pcm

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -77,6 +77,10 @@ begin
       options[:from_stdin] = true
     }
 
+    parser.on('--output-file FILE', 'Resulting image name') {|fn|
+      options[:output_file] = fn
+    }
+
     parser.on('--dinucleotide'){ options[:from_dinucleotide] = true }
   end
   options = cli.parse_options!(argv)
@@ -126,8 +130,18 @@ begin
     end
   end
 
-  in_necessary_orientations(objects_to_render, options[:orientation], logo_folder).each do |infos|
-    filename = File.join(logo_folder, infos[:filename])
+  artifacts = in_necessary_orientations(objects_to_render, options[:orientation], logo_folder)
+
+  if options[:output_file]
+    if artifacts.size == 1
+      # replace name
+      artifacts.first[:filename] = options[:output_file]
+    else
+      raise 'When output file is specified, the only one logo can be rendered'
+    end
+  end
+  artifacts.each do |infos|
+    filename = File.absolute_path(infos[:filename], logo_folder)
     infos[:renderable].render(canvas_factory).write("PNG:#{filename}")
   end
 rescue => err

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.3.0"
+  VERSION = "1.3.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.3.0
+  version: 1.3.1
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-04-17 00:00:00.000000000 Z
+date: 2018-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
@@ -58,6 +58,9 @@ files:
 - TODO.txt
 - bin/glue_logos
 - bin/sequence_logo
+- docker/Dockerfile-rmagick-alpine
+- docker/Dockerfile-rmagick-slim
+- docker/Dockerfile-sequence_logo
 - lib/sequence_logo.rb
 - lib/sequence_logo/alignment.rb
 - lib/sequence_logo/assets/nucl_simpa/a.png
@@ -119,7 +122,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.3
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: Tool for drawing sequence logos of motifs