rbbt-util 5.26.150 → 5.26.151

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ad40e6919c3e8e77360dbfae0ea25c736c6144989517232d958f1438c8f80097
-  data.tar.gz: 825d7c86c2ae9acf7d47341cc9871a9e999e9591cdcdbfc6270e197be156ebae
+  metadata.gz: 11b833bbcd15bc363a8bc7923828bc7545c276f79d9ed2d41a1078e8d57fff10
+  data.tar.gz: 83bfc6713a4333ae904cd8636eb8e9724545085d1c4aff1973b534287521d342
 SHA512:
-  metadata.gz: 34951a010cac42122a179959356a0e8f164489de0de3f04888754826563c156a384af687d7c8119b4ea228a0429db5d7cc1757f60c8ee81117b5ad161d0fc01d
-  data.tar.gz: 7a5ca9c1f0bf6cc2684aecd6a44eb2fe4f777b6c16de2069a01eed8196525e5ec40a521ad9a6b026dba9fd5c44bb63ffc789051eab14d88bd78bc32046565ccf
+  metadata.gz: 23f47354eba951a3d299b132c25e096d6de81e3e1254fda1a5a6b0a245455139c9bfcbf4db4d20ca50b7d91828a04fdca517109235ffd4fae69feb118f252392
+  data.tar.gz: a3fbc000a6626b94da9a6895a473a1300b388e7350d05327cd824e3a027a7ca50c5c761a29fe7c52b39ea66be8e89f81c6c76137ee6283be0a1ad254e95b4960

data/lib/rbbt/util/cmd.rb

@@ -29,7 +29,18 @@ module CMD
           block.call
         end
       end
-      @@init_cmd_tool[tool] = true
+      version_txt = ""
+      %w(--version -version --help).each do |f|
+        begin
+          version_txt += CMD.cmd("#{tool} #{f}").read
+          break
+        rescue
+        end
+      end
+
+      version = Misc.scan_version_text(version_txt, tool)
+
+      @@init_cmd_tool[tool] = version || true
 
       return cmd if cmd
     end
@@ -37,6 +48,11 @@ module CMD
     tool.to_s
   end
 
+  def self.versions
+    return {} unless defined? @@init_cmd_tool
+    @@init_cmd_tool.select{|k,v| v =~ /\d+\./ }
+  end
+
   def self.gzip_pipe(file)
     Open.gzip?(file) ? "<(gunzip -c '#{file}')" : "'#{file}'"
   end
@@ -88,7 +104,7 @@ module CMD
 
     log = true if log.nil?
     
-    if cmd.nil? and ! Symbol === tool 
+    if cmd.nil? && ! Symbol === tool 
       cmd = tool
     else
       tool = get_tool(tool)

data/lib/rbbt/util/misc/inspect.rb

@@ -398,4 +398,11 @@ module Misc
       nil
     end
   end
+
+  def self.scan_version_text(text, cmd = nil)
+    cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
+    m = text.match(/(?:version.*?|#{cmd}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+    return nil if m.nil?
+    m[1]
+  end
 end

data/lib/rbbt/util/version.rb

@@ -41,6 +41,8 @@ module Rbbt
       versions[name] = version
     end
     versions
+
+    versions.merge(CMD.versions)
   end
 
   Rbbt.add_version(__FILE__)

data/lib/rbbt/workflow/step/run.rb

@@ -420,6 +420,7 @@ class Step
           result
         end # END PERSIST
         log :done, "Completed step #{Log.color :yellow, task.name.to_s || ""} in #{time_elapsed.to_i}+#{(total_time_elapsed - time_elapsed).to_i} sec." unless stream or time_elapsed.nil?
+        set_info :versions, Rbbt.versions
 
         if no_load
           @result ||= result

data/test/rbbt/util/test_misc.rb

@@ -626,5 +626,69 @@ EOF
       assert_match /^[0-9a-z]{10,}$/, Misc.file2md5(file)
     end
   end
+
+  def test_scan_version_text
+    txt =<<-EOF
+Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
+Version: 1.10.2-dirty (using htslib 1.10.2-12-gd807564-dirty)
+
+Usage:   bcftools [--version|--version-only] [--help] <command> <argument>
+
+Commands:
+
+ -- Indexing
+    index        index VCF/BCF files
+
+ -- VCF/BCF manipulation
+    annotate     annotate and edit VCF/BCF files
+    concat       concatenate VCF/BCF files from the same set of samples
+    convert      convert VCF/BCF files to different formats and back
+    isec         intersections of VCF/BCF files
+    merge        merge VCF/BCF files files from non-overlapping sample sets
+    norm         left-align and normalize indels
+    plugin       user-defined plugins
+    query        transform VCF/BCF into user-defined formats
+    reheader     modify VCF/BCF header, change sample names
+    sort         sort VCF/BCF file
+    view         VCF/BCF conversion, view, subset and filter VCF/BCF files
+
+ -- VCF/BCF analysis
+    call         SNP/indel calling
+    consensus    create consensus sequence by applying VCF variants
+    cnv          HMM CNV calling
+    csq          call variation consequences
+    filter       filter VCF/BCF files using fixed thresholds
+    gtcheck      check sample concordance, detect sample swaps and contamination
+    mpileup      multi-way pileup producing genotype likelihoods
+    roh          identify runs of autozygosity (HMM)
+    stats        produce VCF/BCF stats
+
+ Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
+ automatically even when streaming from a pipe. Indexed VCF and BCF will work
+ in all situations. Un-indexed VCF and BCF and streams will work in most but
+ not all situations.
+    EOF
+
+    assert_equal "1.10.2-dirty", Misc.scan_version_text(txt, "bcftools")
+
+    txt =<<-EOF
+The Genome Analysis Toolkit (GATK) v4.1.4.1
+HTSJDK Version: 2.21.0
+Picard Version: 2.21.2
+    EOF
+    assert_equal "4.1.4.1", Misc.scan_version_text(txt, "gatk")
+
+
+    txt =<<-EOF
+grep (GNU grep) 3.1
+Copyright (C) 2017 Free Software Foundation, Inc.
+License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+
+Written by Mike Haertel and others, see <http://git.sv.gnu.org/cgit/grep.git/tree/AUTHORS>.
+    EOF
+    assert_equal "3.1", Misc.scan_version_text(txt, "grep")
+  end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.150
+  version: 5.26.151
 platform: ruby
 authors:
 - Miguel Vazquez