rbbt-util 5.23.11 → 5.23.12

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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+ metadata.gz: f6ae6631eb6e9bb1a1b31eb427c4245072253f4f
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+ data.tar.gz: 333e8a20a8a3aa7d631a879d35ff808fb2c51946
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+ metadata.gz: 9328bfdbc4c55e3e567edaaed2e11e0ea4c2b160d88d6bb0eef86b2bb785ec597c57008427b044ea106b288e4956148eedc65bc2f798dda1a3a5c6cdbbfaa944
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+ data.tar.gz: fb7291ccdf11019b1f1053f0867775ed0d6434e81a8c51344cc40d705a1a14922a71d96812d8c4452ee9fbf0be3549c2f284a6e1e9e7ff92d4fb346985952637
@@ -40,7 +40,7 @@ module Resource
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  FileUtils.mkdir_p opt_dir unless File.exist? opt_dir
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- %w(.ld-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
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+ %w(.ld-paths .c-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
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  filename = File.join(opt_dir, file)
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  begin
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  FileUtils.touch filename unless File.exist? filename
@@ -49,6 +49,10 @@ module Resource
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  end
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  end
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+ Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
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+ Misc.env_add('C_INCLULDE_PATH',line.chomp)
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+ end if File.exist? File.join(opt_dir, '.c-paths')
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+
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  Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
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  Misc.env_add('LD_LIBRARY_PATH',line.chomp)
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  Misc.env_add('LD_RUN_PATH',line.chomp)
data/lib/rbbt/workflow.rb CHANGED
@@ -423,7 +423,13 @@ module Workflow
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  end
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  end
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- def self.relocate(listed, real, other)
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+ def self.transplant(listed, real, other)
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+ if listed.nil?
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+ parts = real.split("/")
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+ other_parts = other.split("/")
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+ listed = (other_parts[0..-4] + parts[-3..-1]) * "/"
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+ end
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+
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  sl = listed.split("/", -1)
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  so = other.split("/", -1)
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  sr = real.split("/", -1)
@@ -437,13 +443,19 @@ module Workflow
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  File.join(sr - sl + so)
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  end
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+ def self.relocate(real, other)
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+ preal = real.split(/\/+/)
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+ pother = other.split(/\/+/)
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+ (preal[0..-4] + pother[-3..-1]) * "/"
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+ end
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+
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  def self.load_step(path)
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  step = Step.new path
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  step.dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
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  if File.exists?(dep_path)
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  Workflow.load_step dep_path
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  else
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- new_path = relocate(step.info[:path], path, dep_path)
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+ new_path = relocate(path, dep_path)
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  Workflow.load_step new_path
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  end
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  end
@@ -163,6 +163,7 @@ class Step
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  def set_info(key, value)
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  return nil if @exec or info_file.nil?
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+ return nil if ! File.writable? info_file
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  value = Annotated.purge value if defined? Annotated
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  Open.lock(info_file, :lock => info_lock) do
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  i = info(false).dup
@@ -621,7 +621,7 @@ class Step
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  def join
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- grace
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+ grace if Open.exists?(info_file)
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  if streaming?
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  join_stream
@@ -126,10 +126,20 @@ build_dir(){
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  compile(){
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  local name=$1; shift
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  local extra="$@"
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- [ -f Makefile ] && make && make install
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- [ -f build.xml ] && ant
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- [ -f setup.rb ] && ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra
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- [ -f setup.py ] && python setup.py build && python setup.py install --user && clean_build
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+
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+ if [ -f Makefile -o -f makefile ]; then
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+ make || exit -1
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+ make install || echo "No install"
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+ fi
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+
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+ [ -f build.xml ] && (ant || exit -1)
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+
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+ [ -f setup.rb ] && (ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra || exit -1)
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+
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+ if [ -f setup.py ]; then
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+ python setup.py build && python setup.py install --user || exit -1
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+ clean_build
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+ fi
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  }
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  build(){
@@ -140,7 +150,7 @@ build(){
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  local old_pwd="`expand_path $(pwd)`"
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  cd "`build_dir`"
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- echo `pwd`
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+ echo PWD: `pwd`
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  ls
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  if [ -f Makefile.am -a ! -f configure ]; then
@@ -164,6 +174,7 @@ build(){
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  compile "$name" $extra
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  setup "$name"
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  clean_build
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+ cd "$old_pwd"
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  else
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  compile "$name" $extra
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  move_opt "$name"
@@ -171,7 +182,6 @@ build(){
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  clean_build
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  fi
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- cd "$old_pwd"
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  }
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  #{{{ SETUP
@@ -277,7 +277,27 @@ class TestWorkflow < Test::Unit::TestCase
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  other = '/home/user/.rbbt/var/jobs/TestWF/task2/Default'
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  real_other = '/usr/local/var/rbbt/jobs/TestWF/task2/Default'
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- assert_equal real_other, Workflow.relocate(listed, real, other)
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+ assert_equal real_other, Workflow.relocate(real, other)
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+ assert_equal real_other, Workflow.relocate(real, other)
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+ end
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+
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+ def test_transplant
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+ listed = '/home/user/.rbbt/var/jobs/TestWF/task1/Default'
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+ real = '/usr/local/var/rbbt/jobs/TestWF/task1/Default'
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+ other = '/home/user/.rbbt/var/jobs/TestWF/task2/Default'
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+ real_other = '/usr/local/var/rbbt/jobs/TestWF/task2/Default'
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+
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+ assert_equal real_other, Workflow.transplant(listed, real, other)
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+ assert_equal real_other, Workflow.transplant(nil, real, other)
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+ end
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+
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+ def test_relocate_alt
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+ listed = '/scratch/tmp/rbbt/.rbbt/var/jobs/Study/sample_gene_cnvs_focal/Bladder-TCC'
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+ real = '/home/bsc26/bsc26892/.rbbt/var/jobs/Study/sample_gene_cnvs_focal/Bladder-TCC'
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+ other = '/scratch/tmp/rbbt/scratch/bsc26892/rbbt/var/jobs/Sample/gene_cnv_status_focal/PCAWG'
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+ real_other = '/home/bsc26/bsc26892/.rbbt/var/jobs/Sample/gene_cnv_status_focal/PCAWG'
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+
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+ assert_equal real_other, Workflow.relocate(real, other)
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  end
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-util
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  version: !ruby/object:Gem::Version
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- version: 5.23.11
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+ version: 5.23.12
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2018-08-09 00:00:00.000000000 Z
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+ date: 2018-08-10 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake