rbbt-util 5.26.43 → 5.26.44

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 37a031122ec367f6a6f83e33039f26ea21cb2da73df6c251af56bc4568e1ad13
+  metadata.gz: ee472bbeb2d0541575f941de8d4449565c0b5749edba5e939a703f006dfbf9dd
+  data.tar.gz: cbbf92b94071ec10e304ccec236458b12e19ea3ffad22ddc07b30250bbb6a4d0
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-  data.tar.gz: 4b7df1c8f10e5aaa30789ec4bd3d1b2a3513ba4d0e5a3a1db5cf94e94876953cdff2518888cde57a204389c26390921e0620827f6145f57780109ff63ccf76b3
+  metadata.gz: 146f93aa1f32c53b88097f1dfa75721c6384395dd2f09c3a9240b04918250d42c32e6ef7b4420d95d7ef18ede20226c2f762ef3a04fec636f48c4fd99bf5db2b
+  data.tar.gz: c302243845ea9de591ef0486d8e80b44b757103a50a0edf51b59103e8d48a0e44cc3a3695198412cfa091f2ad23ba1110d9f9faf5b08c277a7e091a1839b2f41

data/lib/rbbt/hpc.rb

@@ -125,7 +125,7 @@ module load intel/2018.1
 module load singularity
 PROJECTS_ROOT="/gpfs/projects/bsc26/"
 SINGULARITY_IMG="$PROJECTS_ROOT/rbbt.singularity.img"
-SINGULARITY_OVERLAY_DIR="$PROJECTS_ROOT/rbbt.singularity.overlays"
+SINGULARITY_OPT_DIR="$PROJECTS_ROOT/singularity_opt/"
 SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
 mkdir -p "$SINGULARITY_RUBY_INLINE"
         EOF
@@ -182,9 +182,6 @@ echo "/scratch/tmp/rbbt/projects/rbbt/workflows/" > $CONTAINER_DIR/.rbbt/etc/wor
 # Copy image
 rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img" 1>&2
 SINGULARITY_IMG="$CONTAINER_DIR/rbbt.singularity.img"
-
-rsync -avz "$SINGULARITY_OVERLAY_DIR"/ "$CONTAINER_DIR/rbbt.singularity.overlays/" 1>&2
-SINGULARITY_OVERLAY_DIR="$CONTAINER_DIR/rbbt.singularity.overlays"
 EOF
         end
 
@@ -206,11 +203,10 @@ EOF
       exec_cmd = %(env _JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m")
 
       if singularity
-        singularity_exec = %(singularity exec -e $(for f in `ls $SINGULARITY_OVERLAY_DIR/*.img`; do  echo -n  --overlay "\"$f\" "; done) )
+        singularity_exec = %(singularity exec -e -B $SINGULARITY_OPT:/singularity_opt/ -B /apps/)
 
         if contain
           singularity_exec << %( -C -H "$CONTAINER_DIR" \
--B /apps/ \
 -B /scratch/tmp \
 -B "$SINGULARITY_RUBY_INLINE":"$CONTAINER_DIR/.ruby_inline":rw  \
 -B ~/git:"$CONTAINER_DIR/git":ro \
@@ -221,7 +217,7 @@ EOF
 "$SINGULARITY_IMG")
           exec_cmd << ' TMPDIR="$CONTAINER_DIR/.rbbt/tmp" '
         else
-          singularity_exec += %( -B /apps/ -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG" )
+          singularity_exec += %( -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG" )
         end
 
         if development

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.43
+  version: 5.26.44
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-24 00:00:00.000000000 Z
+date: 2019-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake