rbbt-util 5.31.3 → 5.31.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d850d97bff4cc0cd4123cbfdd2301c8d777fda47e6767542b6e3d9dc8ed22501
-  data.tar.gz: df69bfc3ca3b2605dd0171dd553ddf0f6dd0c064bf1fe66c5c9e8909d23760d8
+  metadata.gz: 9627d833faf734e912d68d60714081cd8179b8f65de153842c2a77bc356e58ab
+  data.tar.gz: 4d75542d741d61732ddead0ab6295e97461e5cd4aa7b8baeb4436f78f875465d
 SHA512:
-  metadata.gz: 2ae6c6d6d098043d8117eadfcfb47dbc97d2dcc7af2ffa96775d8ba54fc2ec0b063311db6a3ba8c48f6c0d11d066ab2182676b6c87a4aa3075bd695ff4ca57cb
-  data.tar.gz: 3de13554f1066d6fa7ee8be74842dcc4b4bbadbe422ca943c7ca272fe735643673067841cff077c9ea1c9eb39d5d1641dd91e3926a4b276fa80815baf17cf31a
+  metadata.gz: 7105097e07ee1da675b2ee4cc5fa7f7be61bd49051553a28ca39a829105fda3e08e684ea804928000863d83d67bdad3d462121ab23a379a5ba76d3ce4c74ccc5
+  data.tar.gz: ba67880edc6ecad00c8a06fa802fc56a035524a321ab31abe8d4cae07ea521ce641abd948731cd7da8f0582b8d5ea9cdea8bca3e9152acb070f379b35fd0a40d

data/lib/rbbt/hpc/batch.rb

@@ -11,30 +11,35 @@ module HPC
       env_cmd     = Misc.process_options options, :env_cmd
       development = Misc.process_options options, :development
 
+      if contain = options[:contain]
+        contain = File.expand_path(contain)
+        env_cmd ||= ""
+        env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
+      end
+
       if options[:singularity]
 
         group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir
 
         singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline
 
-        singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B /apps/) 
+        singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B "#{singularity_ruby_inline}":"/.singularity_ruby_inline":rw ) 
 
-        if contain = options[:contain]
-          contain = File.expand_path(contain)
+        if contain && options[:hardened]
           singularity_cmd << %( -C -H "#{contain}" \
+-B "/.singularity_ruby_inline":"#{contain}/.singularity_ruby_inline":rw 
 -B "#{options[:batch_dir]}" \
 -B /scratch/tmp \
 #{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
 -B #{scratch_group_dir} \
 -B #{projects_group_dir} \
--B "#{singularity_ruby_inline}":"#{contain}/.ruby_inline":rw  \
+-B /apps/ \
 -B ~/git:"#{contain}/git":ro \
 #{Open.exists?('~/.rbbt/software/opt/')? '-B ~/.rbbt/software/opt/:"/opt/":ro' : '' } \
 -B ~/.rbbt:"#{contain}/home/":ro)
-          singularity_cmd << " #{singularity_img} "
         end
-        env_cmd ||= ""
-        env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
+
+        singularity_cmd << " #{singularity_img} "
       end
 
       if env_cmd
@@ -170,7 +175,7 @@ EOF
         batch_options[:wipe_container] ||= 'post'
       end
 
-      if batch_options[:contain] && ! batch_options[:singularity]
+      if batch_options[:contain] && ! batch_options[:hardened]
         options[:workdir_all] = batch_options[:contain]
       end
 
@@ -304,7 +309,7 @@ module load singularity
 mkdir -p "#{singularity_opt_dir}"
         EOF
 
-        if contain
+        if contain && options[:hardened]
 
           prepare_environment +=<<-EOF
 # Prepare container for singularity

data/lib/rbbt/hpc/lsf.rb

@@ -7,7 +7,8 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-MAX_MEMORY=$LSB_MAX_MEM_RUSAGE || let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
+[[ -z $LSB_MAX_MEM_RUSAGE ]] || MAX_MEMORY=$LSB_MAX_MEM_RUSAGE 
+[[ -z $MAX_MEMORY ]] && let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
 BATCH_JOB_ID=$LSF_JOBID
 BATCH_SYSTEM=LSF
       EOF

data/lib/rbbt/resource/util.rb

@@ -33,7 +33,7 @@ end
 
 module Resource
   def set_software_env(software_dir)
-    software_dir.find_all.reverse.each do |software_dir|
+    software_dir.opt.find_all.collect{|d| d.annotate(File.dirname(d)) }.reverse.each do |software_dir|
       next unless software_dir.exists?
       software_dir = File.expand_path(software_dir)
       opt_dir = File.join(software_dir, 'opt')

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

@@ -99,6 +99,7 @@ class Step
         if String === value && File.exists?(value)
           Open.ln_s(value, path)
         else
+          value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value
           value = "#{value}" if Path === value
           Open.write(path + '.yaml', value.to_yaml)
         end

data/share/install/software/lib/install_helpers

@@ -147,6 +147,8 @@ get_git(){
           git pull origin master
           git rebase master
           git stash apply
+          git submodule init
+          git submodule update
         fi
     else
       if [ $version == 'none' ];then
@@ -154,6 +156,10 @@ get_git(){
       else
         git clone --recursive "$url" "$name" -b $version
       fi
+
+      cd "$name" 
+      git submodule init
+      git submodule update
     fi
 
     clean_build

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.3
+  version: 5.31.9
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-25 00:00:00.000000000 Z
+date: 2021-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake