rbbt-util 5.26.39 → 5.26.40

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 5325deee00f67d664dd952f2c3e8e06d8ff2122c7aea2401a9ea259818e60cd4
+  metadata.gz: c402dd55adf3e0a67b17b70c55550033e5c49d8662d9a299fb11247c602b4d9a
+  data.tar.gz: 48bea651b2efa8ef85e0dd34cfccd3ceb446dd4353c41a482fe8ba08b382f88b
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+  metadata.gz: 96cfd11c662b6fb442687fd1b545344ef9c1834f8800bd9cd29985507824df45fe3ab2d6b68c2d9ee03bb696aae287dc6e877b154c65e5f3fb5c27a1adba35a4
+  data.tar.gz: a6b4eee7818f876694d30050044cd2ae885eb2c52f32ba3dd41444904d9e4ef4bbfeaa09a49a3f7b38f94e15c2e81f5d4295c0c25c0c6d0ac1590a6da8bc6aeb

data/lib/rbbt/hpc.rb

@@ -123,8 +123,9 @@ let "MAX_MEMORY=$SLURM_MEM_PER_CPU * $SLURM_CPUS_ON_NODE"
         env +=<<-EOF
 module load intel/2018.1
 module load singularity
-SINGULARITY_IMG="$HOME/projects/rbbt.singularity.img"
-SINGULARITY_OVERLAY_DIR="$HOME/projects/rbbt.singularity.overlays"
+PROJECTS_ROOT="/gpfs/projects/bsc26/"
+SINGULARITY_IMG="$PROJECTS_ROOT/rbbt.singularity.img"
+SINGULARITY_OVERLAY_DIR="$PROJECTS_ROOT/rbbt.singularity.overlays"
 SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
 mkdir -p "$SINGULARITY_RUBY_INLINE"
         EOF
@@ -181,6 +182,9 @@ 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
 
@@ -202,7 +206,7 @@ EOF
       exec_cmd = %(env _JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m")
 
       if singularity
-        singularity_exec = %(singularity exec -e $(ls $SINGULARITY_OVERLAY_DIR/*.img  |xargs -l echo -n " " --overlay) )
+        singularity_exec = %(singularity exec -e $(for f in `ls $SINGULARITY_OVERLAY_DIR/*.img`; do  echo -n  --overlay "'$f' "; done) )
 
         if contain
           singularity_exec << %( -C -H "$CONTAINER_DIR" \

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.39
+  version: 5.26.40
 platform: ruby
 authors:
 - Miguel Vazquez