rbbt-util 5.31.4 → 5.31.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 346571583494c278a4499a2ad2bddc248af37176a7acb3a2457af05941b7a074
-  data.tar.gz: 32539316c53ef634de003ea246e8a649de978f66ea48e9666218eac51f85f4b6
+  metadata.gz: 4909a13c518c1128adcdfc981153c04bb9f57c11b8501c65549b427fd0d647d5
+  data.tar.gz: 0b6f7089d1c78aec899dcfdec1784a0bbb56f3df7c84f24bedb6da0d79e058fc
 SHA512:
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-  data.tar.gz: 3ef61d067b36a953fd284954db046607de7050a933461a0ebc8b7096abe9d943527165337cf375b43e5f97d20b2ee27722c603684a4e1e63fb20bec56d57dc13
+  metadata.gz: f041b99830f23f3bd8f6e29de8bec29ca5352d4a0873d36dc452b5c1d7a2d31a7d563247337980e8df06fbd9a1835ba04bab43bd9293d9484f82ab00fc534482
+  data.tar.gz: 2c80efb6433e60851c666cc7bb75a7e66a7a3e5813db3bd41c73c8511ef94a64b4ab8528da2a2abe104f2aad97d7ed69876931e5932c02a7ed2db1e5f470a3b1

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/util/cmd.rb

@@ -10,6 +10,14 @@ module CMD
     TOOLS[tool] = [claim, test, block, cmd]
   end
 
+  def self.conda(tool, env = nil, channel = 'bioconda')
+    if env
+      CMD.cmd("bash -l -c '(conda activate #{env} && conda install #{tool} -c #{channel})'")      
+    else
+      CMD.cmd("bash -l -c 'conda install #{tool} -c #{channel}'")      
+    end
+  end
+
   def self.get_tool(tool)
     return tool.to_s unless TOOLS[tool]
 

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

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.4
+  version: 5.31.10
 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