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 +4 -4
- data/lib/rbbt/resource/util.rb +5 -1
- data/lib/rbbt/workflow.rb +14 -2
- data/lib/rbbt/workflow/accessor.rb +1 -0
- data/lib/rbbt/workflow/step/run.rb +1 -1
- data/share/install/software/lib/install_helpers +16 -6
- data/test/rbbt/test_workflow.rb +21 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: f6ae6631eb6e9bb1a1b31eb427c4245072253f4f
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data.tar.gz: 333e8a20a8a3aa7d631a879d35ff808fb2c51946
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9328bfdbc4c55e3e567edaaed2e11e0ea4c2b160d88d6bb0eef86b2bb785ec597c57008427b044ea106b288e4956148eedc65bc2f798dda1a3a5c6cdbbfaa944
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data.tar.gz: fb7291ccdf11019b1f1053f0867775ed0d6434e81a8c51344cc40d705a1a14922a71d96812d8c4452ee9fbf0be3549c2f284a6e1e9e7ff92d4fb346985952637
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data/lib/rbbt/resource/util.rb
CHANGED
@@ -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
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@@ -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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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)
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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.
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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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sl = listed.split("/", -1)
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so = other.split("/", -1)
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sr = real.split("/", -1)
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@@ -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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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(
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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
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@@ -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
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@@ -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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-
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[ -f
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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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[ -f build.xml ] && (ant || exit -1)
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[ -f setup.rb ] && (ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra || exit -1)
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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(){
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@@ -140,7 +150,7 @@ build(){
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local old_pwd="`expand_path $(pwd)`"
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cd "`build_dir`"
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echo `pwd`
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echo PWD: `pwd`
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ls
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if [ -f Makefile.am -a ! -f configure ]; then
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compile "$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"
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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
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data/test/rbbt/test_workflow.rb
CHANGED
@@ -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(
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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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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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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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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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assert_equal real_other, Workflow.relocate(real, other)
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end
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end
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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.
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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-
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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
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