rbbt-util 5.23.11 → 5.23.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: aa7c357c654a8b1863b86fa0bf3d6f8b8051ec35
-  data.tar.gz: 14da2501042aefc371c57f23eaf73932ae33b536
+  metadata.gz: f6ae6631eb6e9bb1a1b31eb427c4245072253f4f
+  data.tar.gz: 333e8a20a8a3aa7d631a879d35ff808fb2c51946
 SHA512:
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-  data.tar.gz: f52c250423ebf350a3a39e326d143ecc0854b0be0e0b770ab4d376d1703f7639059bd2892b8c234b712faf72ec74612af929829b33ad26c3909e11dc34d7f119
+  metadata.gz: 9328bfdbc4c55e3e567edaaed2e11e0ea4c2b160d88d6bb0eef86b2bb785ec597c57008427b044ea106b288e4956148eedc65bc2f798dda1a3a5c6cdbbfaa944
+  data.tar.gz: fb7291ccdf11019b1f1053f0867775ed0d6434e81a8c51344cc40d705a1a14922a71d96812d8c4452ee9fbf0be3549c2f284a6e1e9e7ff92d4fb346985952637

data/lib/rbbt/resource/util.rb

@@ -40,7 +40,7 @@ module Resource
 
       FileUtils.mkdir_p opt_dir unless File.exist? opt_dir
 
-      %w(.ld-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
+      %w(.ld-paths .c-paths .pkgconfig-paths .aclocal-paths .java-classpaths).each do |file|
         filename = File.join(opt_dir, file)
         begin
           FileUtils.touch filename unless File.exist? filename
@@ -49,6 +49,10 @@ module Resource
         end
       end
 
+      Open.read(File.join opt_dir, '.c-paths').split(/\n/).each do |line|
+        Misc.env_add('C_INCLULDE_PATH',line.chomp)
+      end if File.exist? File.join(opt_dir, '.c-paths')
+
       Open.read(File.join opt_dir, '.ld-paths').split(/\n/).each do |line|
         Misc.env_add('LD_LIBRARY_PATH',line.chomp)
         Misc.env_add('LD_RUN_PATH',line.chomp)

data/lib/rbbt/workflow.rb

@@ -423,7 +423,13 @@ module Workflow
     end
   end
 
-  def self.relocate(listed, real, other)
+  def self.transplant(listed, real, other)
+    if listed.nil?
+      parts = real.split("/")
+      other_parts = other.split("/")
+      listed = (other_parts[0..-4] + parts[-3..-1]) * "/"
+    end
+
     sl = listed.split("/", -1)
     so = other.split("/", -1)
     sr = real.split("/", -1)
@@ -437,13 +443,19 @@ module Workflow
     File.join(sr - sl + so)
   end
 
+  def  self.relocate(real, other)
+    preal = real.split(/\/+/)
+    pother = other.split(/\/+/)
+    (preal[0..-4] + pother[-3..-1]) * "/"
+  end
+
   def self.load_step(path)
     step = Step.new path
     step.dependencies = (step.info[:dependencies] || []).collect do |task,name,dep_path|
       if File.exists?(dep_path)
         Workflow.load_step dep_path
       else
-        new_path = relocate(step.info[:path], path, dep_path)
+        new_path = relocate(path, dep_path)
         Workflow.load_step new_path
       end
     end

data/lib/rbbt/workflow/accessor.rb

@@ -163,6 +163,7 @@ class Step
 
   def set_info(key, value)
     return nil if @exec or info_file.nil?
+    return nil if ! File.writable? info_file
     value = Annotated.purge value if defined? Annotated
     Open.lock(info_file, :lock => info_lock) do
       i = info(false).dup

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

@@ -621,7 +621,7 @@ class Step
 
   def join
 
-    grace
+    grace if Open.exists?(info_file) 
 
     if streaming?
       join_stream 

data/share/install/software/lib/install_helpers

@@ -126,10 +126,20 @@ build_dir(){
 compile(){
     local name=$1; shift
     local extra="$@"
-    [ -f Makefile ] && make && make install
-    [ -f build.xml ] && ant
-    [ -f setup.rb ] && ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra
-    [ -f setup.py ] && python setup.py build &&  python setup.py install --user && clean_build
+
+    if [ -f Makefile -o -f makefile ]; then
+        make || exit -1
+        make install || echo "No install"
+    fi
+
+    [ -f build.xml ] && (ant || exit -1)
+
+    [ -f setup.rb ] && (ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra || exit -1)
+
+    if [ -f setup.py ]; then 
+        python setup.py build &&  python setup.py install --user || exit -1
+        clean_build 
+    fi
 }
 
 build(){
@@ -140,7 +150,7 @@ build(){
 
     local old_pwd="`expand_path $(pwd)`"
     cd "`build_dir`"
-    echo `pwd`
+    echo PWD: `pwd`
     ls
 
     if [ -f Makefile.am -a ! -f configure ]; then
@@ -164,6 +174,7 @@ build(){
         compile "$name" $extra
         setup "$name"
         clean_build
+        cd "$old_pwd"
     else
         compile "$name" $extra
         move_opt "$name"
@@ -171,7 +182,6 @@ build(){
         clean_build
     fi
     
-    cd "$old_pwd"
 }
 
 #{{{ SETUP

data/test/rbbt/test_workflow.rb

@@ -277,7 +277,27 @@ class TestWorkflow < Test::Unit::TestCase
     other = '/home/user/.rbbt/var/jobs/TestWF/task2/Default'
     real_other = '/usr/local/var/rbbt/jobs/TestWF/task2/Default'
 
-    assert_equal real_other, Workflow.relocate(listed, real, other)
+    assert_equal real_other, Workflow.relocate(real, other)
+    assert_equal real_other, Workflow.relocate(real, other)
+  end
+
+  def test_transplant
+    listed = '/home/user/.rbbt/var/jobs/TestWF/task1/Default'
+    real = '/usr/local/var/rbbt/jobs/TestWF/task1/Default'
+    other = '/home/user/.rbbt/var/jobs/TestWF/task2/Default'
+    real_other = '/usr/local/var/rbbt/jobs/TestWF/task2/Default'
+
+    assert_equal real_other, Workflow.transplant(listed, real, other)
+    assert_equal real_other, Workflow.transplant(nil, real, other)
+  end
+
+  def test_relocate_alt
+    listed = '/scratch/tmp/rbbt/.rbbt/var/jobs/Study/sample_gene_cnvs_focal/Bladder-TCC'
+    real = '/home/bsc26/bsc26892/.rbbt/var/jobs/Study/sample_gene_cnvs_focal/Bladder-TCC'
+    other = '/scratch/tmp/rbbt/scratch/bsc26892/rbbt/var/jobs/Sample/gene_cnv_status_focal/PCAWG'
+    real_other = '/home/bsc26/bsc26892/.rbbt/var/jobs/Sample/gene_cnv_status_focal/PCAWG'
+
+    assert_equal real_other, Workflow.relocate(real, other)
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.11
+  version: 5.23.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-09 00:00:00.000000000 Z
+date: 2018-08-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake