rbbt-util 5.25.17 → 5.25.18

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d49ac1028fd178503c70f32280d08e8fd66b11af
-  data.tar.gz: 1c5cffa02dd06ffc3b13c10abaf9dd15d8bea9bf
+  metadata.gz: 32456b2f23ba8e3a018ae100b41b565a04284ccf
+  data.tar.gz: '0646998ae0c7d8ed85eef12e028e7e57ace7c380'
 SHA512:
-  metadata.gz: 64e6b2373c856bdd90c04bc074c43749051725bbf9ed23e38c28cf3b18c68b23278f26e3ef5b85b628d4f91b5085e28497b97136dd4274e04c70c8a2be6bc881
-  data.tar.gz: 4b11f0ee0e406d64d6412278f349a156b4e4cf52f720eef958e9c118be4ca7a84ac9c4c8dc1c63a7bef80f21d4fa0b1feaf1b1641b2678433b785fe587f3b480
+  metadata.gz: c1fa0f6562f1ed28a8d932372ab7cb6991d28c7587586e10d5e4a9235c5f045f9b7ba2dc8a7620d998c24b3f129dae89f7d6ce9950926ece5eeeed23ca097403
+  data.tar.gz: 2392d0dce826ea7e4c02da67a07e3fc7e11df664564ecc264946214327d1e3ddcbb68021dba50a791740e8b2bd93d0b475dca9e1bdb260cab318bb68148a82aa

data/lib/rbbt/hpc.rb

@@ -99,7 +99,6 @@ module load java
         env +=<<-EOF
 module load intel/2018.1
 module load singularity
-module load samtools
 SINGULARITY_IMG="$HOME/projects/rbbt.singularity.img"
 SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
 mkdir -p "$SINGULARITY_RUBY_INLINE"
@@ -356,7 +355,9 @@ EOF
       task = job.task_name
       name = job.clean_name
       keep_workdir = options.delete :keep_SLURM_workdir 
-      TmpFile.with_file(nil, !keep_workdir) do |tmp_directory|
+      slurm_basedir = options.delete :SLURM_basedir
+      slurm_basedir = "~/rbbt-workdir" if slurm_basedir.nil?
+      TmpFile.with_file(nil, !keep_workdir, :tmpdir => slurm_basedir, :prefix => "SLURM_rbbt_job-") do |tmp_directory|
         workdir = options[:workdir] ||= File.join(tmp_directory, 'workdir')
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
         Step.save_job_inputs(job, inputs_dir)

data/lib/rbbt/util/tmpfile.rb

@@ -23,8 +23,8 @@ module TmpFile
   end
 
   # Creates a random filename in the temporary directory
-  def self.tmp_file(s = "",max=10000000)
-    File.join(TMPDIR, random_name(s,max))
+  def self.tmp_file(s = "", max=10000000, dir = TMPDIR)
+    File.expand_path(File.join(dir, random_name(s,max)))
   end
 
   def self.with_file(content = nil, erase = true, options = {})
@@ -32,7 +32,9 @@ module TmpFile
     options, erase = erase, true if Hash === erase 
 
     prefix = options[:prefix] || ""
-    tmpfile = tmp_file prefix
+    tmpdir = options[:tmpdir] || TMPDIR
+    max = options[:max] || 10000000
+    tmpfile = tmp_file prefix, max, tmpdir
     if options[:extension]
       tmpfile += ".#{options[:extension]}"
     end

data/share/install/software/lib/install_helpers

@@ -100,20 +100,32 @@ get_git(){
     local name="$1"
     local url="$2"
 
+    if [[ "$url" == *" "* ]]; then
+      version="${url/* /}"
+      url="${url/ */}"
+      echo "Using version $version of repo $url"
+    else
+      version='none'
+    fi
+
     local old_pwd="`expand_path $(pwd)`"
 
     cd $OPT_SCM_DIR
     if [ -d "$name" ]; then
         cd "$name" 
 
-        if [ ! "$NOWEB" == "true" ]; then
+        if [ ! "$NOWEB" == "true" -a $version == 'none' ]; then
           git stash
           git pull origin master
           git rebase master
           git stash apply
         fi
     else
+      if [ $version == 'none' ];then
         git clone "$url" "$name"
+      else
+        git clone "$url" "$name" -b $version
+      fi
     fi
 
     clean_build
@@ -202,28 +214,32 @@ build(){
     fi
 
     if [ -f CMakeLists.txt ]; then
-        mkdir build
-        cd build
-        cmake -DCMAKE_INSTALL_PREFIX:PATH=/ ..
-        make -j4
-        make DESTDIR="$(opt_dir "$name")" install
-        setup "$name"
-        clean_build
-    fi
-    
-    if [ -f configure ]; then 
+      [ -d build ] || mkdir build
+      cd build
+      cmake -DCMAKE_INSTALL_PREFIX:PATH=/install_dir ..
+      make DESTDIR="$(opt_dir "$name")"  -j4
+      make DESTDIR="$(opt_dir "$name")" install || (cd .. ; mv build "$(opt_dir "$name")")
+      if [ -d "$(opt_dir "$name")/install_dir" ]; then
+        mv "$(opt_dir "$name")/install_dir"/** "$(opt_dir "$name")"
+        rmdir "$(opt_dir "$name")/install_dir"
+      fi
+
+      setup "$name"
+      clean_build
+    else
+      if [ -f configure ]; then 
         echo ./configure --prefix="$(opt_dir "$name")" $extra
         ./configure --prefix="$(opt_dir "$name")" $extra
         compile "$name" $extra
         setup "$name"
         clean_build
-    else
+      else
         compile "$name" $extra
         move_opt "$name"
         setup "$name"
         clean_build
+      fi
     fi
-
     
     cd "$old_pwd"
 }

data/test/rbbt/util/test_tmpfile.rb

@@ -5,7 +5,7 @@ require 'test/unit'
 class TestTmpFile < Test::Unit::TestCase
 
   def test_tmp_file
-    assert(TmpFile.tmp_file("test") =~ /tmp\/test\d+$/)
+    assert(TmpFile.tmp_file("test") =~ /(tmpfiles|tmp)\/test\d+$/)
   end
 
   def test_do_tmp_file
@@ -19,7 +19,12 @@ class TestTmpFile < Test::Unit::TestCase
     TmpFile.with_file(nil, true, :extension => 'txt') do |file|
       assert file =~ /\.txt$/
     end
+  end
 
+  def test_tmpdir
+    TmpFile.with_file(nil, true, :tmpdir => 'TMPDIR') do |file|
+      assert file =~ /TMPDIR/
+    end
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.17
+  version: 5.25.18
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-10 00:00:00.000000000 Z
+date: 2019-01-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake