rbbt-util 5.25.39 → 5.25.40

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0c333ea486edd8afead278153fec7a4c81e2a12e
+  metadata.gz: 9433fb814b44267945865834fea4990b38cbeb96
+  data.tar.gz: 1f1a04136934f52f3a3ff4d7826b2e34a7cddff1
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+  metadata.gz: a5d6572ac860c7028a6abd78fe0bb8cc9e3ca563eccda0e11d404a665a15e29b5a7e5aba43193ed78325e7c92f16dcbeabf876eea28e33c39859737313e76b07
+  data.tar.gz: 2db09b238b2d769ee4b686ca13bc3d9c636af2c3a08512e2adac5801887ec75553a27c4bb038eed17d24fe9117911b337f6c51f17f87ed168de1523b43635108

data/lib/rbbt/hpc.rb

@@ -98,6 +98,9 @@ module Marenostrum
 # Prepare env
 [[ -f ~/config/load.sh ]] && source ~/config/load.sh
 module load java
+
+# Calculate max available memory
+let "MAX_MEMORY=$SLURM_MEM_PER_CPU * $SLURM_CPUS_ON_NODE"
       EOF
 
       if singularity
@@ -165,16 +168,16 @@ EOF
           group = File.basename(File.dirname(ENV['HOME']))
           scratch_group_dir = File.join('/gpfs/scratch/', group)
           projects_group_dir = File.join('/gpfs/projects/', group)
-          exec_cmd = %(singularity exec -e -C -H "$CONTAINER_DIR" -B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$CONTAINER_DIR/.ruby_inline":rw  -B ~/git:"$CONTAINER_DIR/git":ro -B #{scratch_group_dir}:"$CONTAINER_DIR/scratch":ro -B ~/.rbbt/software/opt/:"/opt/":ro  -B ~/.rbbt:"$CONTAINER_DIR/home/":ro -B #{projects_group_dir}:"$CONTAINER_DIR/projects":ro "$SINGULARITY_IMG" env TMPDIR="$CONTAINER_DIR/.rbbt/tmp" rbbt)
+          exec_cmd = %(singularity exec -e -C -H "$CONTAINER_DIR" -B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$CONTAINER_DIR/.ruby_inline":rw  -B ~/git:"$CONTAINER_DIR/git":ro -B #{scratch_group_dir}:"$CONTAINER_DIR/scratch":ro -B ~/.rbbt/software/opt/:"/opt/":ro  -B ~/.rbbt:"$CONTAINER_DIR/home/":ro -B #{projects_group_dir}:"$CONTAINER_DIR/projects":ro "$SINGULARITY_IMG" env TMPDIR="$CONTAINER_DIR/.rbbt/tmp" env _JAVA_OPTION="-Xms1g -Xmx${MAX_MEMORY}m" rbbt)
         else
-          exec_cmd = %(singularity exec -e -B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG" rbbt)
+          exec_cmd = %(singularity exec -e -B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG" env _JAVA_OPTION="-Xms1g -Xmx${MAX_MEMORY}m" rbbt)
         end
 
         if development
           exec_cmd += ' --dev=git'
         end
       else
-        exec_cmd = %(~/git/rbbt-util/bin/rbbt --dev=~/git/)
+        exec_cmd = %(env _JAVA_OPTION="-Xms1g -Xmx${MAX_MEMORY}m" ~/git/rbbt-util/bin/rbbt --dev=~/git/)
       end
 
 

data/share/rbbt_commands/tsv/subset

@@ -16,6 +16,7 @@ Subsets entries from a TSV file from a given list. Works with Tokyocabinet HDB a
 -tcb--tokyocabinet_bd File is a TC BDB
 -hh--header_hash* Change the character used to mark the header line (defaults to #)
 -s--subset* Subset of keys (Comma-separated or file)
+-m--merge Merge TSV rows
 -h--help Help
 EOF
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.39
+  version: 5.25.40
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-01 00:00:00.000000000 Z
+date: 2019-04-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake