rbbt-util 5.26.43 → 5.26.44
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +3 -7
- metadata +2 -2
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: ee472bbeb2d0541575f941de8d4449565c0b5749edba5e939a703f006dfbf9dd
|
|
4
|
+
data.tar.gz: cbbf92b94071ec10e304ccec236458b12e19ea3ffad22ddc07b30250bbb6a4d0
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 146f93aa1f32c53b88097f1dfa75721c6384395dd2f09c3a9240b04918250d42c32e6ef7b4420d95d7ef18ede20226c2f762ef3a04fec636f48c4fd99bf5db2b
|
|
7
|
+
data.tar.gz: c302243845ea9de591ef0486d8e80b44b757103a50a0edf51b59103e8d48a0e44cc3a3695198412cfa091f2ad23ba1110d9f9faf5b08c277a7e091a1839b2f41
|
data/lib/rbbt/hpc.rb
CHANGED
|
@@ -125,7 +125,7 @@ module load intel/2018.1
|
|
|
125
125
|
module load singularity
|
|
126
126
|
PROJECTS_ROOT="/gpfs/projects/bsc26/"
|
|
127
127
|
SINGULARITY_IMG="$PROJECTS_ROOT/rbbt.singularity.img"
|
|
128
|
-
|
|
128
|
+
SINGULARITY_OPT_DIR="$PROJECTS_ROOT/singularity_opt/"
|
|
129
129
|
SINGULARITY_RUBY_INLINE="$HOME/.singularity_ruby_inline"
|
|
130
130
|
mkdir -p "$SINGULARITY_RUBY_INLINE"
|
|
131
131
|
EOF
|
|
@@ -182,9 +182,6 @@ echo "/scratch/tmp/rbbt/projects/rbbt/workflows/" > $CONTAINER_DIR/.rbbt/etc/wor
|
|
|
182
182
|
# Copy image
|
|
183
183
|
rsync -avz "$SINGULARITY_IMG" "$CONTAINER_DIR/rbbt.singularity.img" 1>&2
|
|
184
184
|
SINGULARITY_IMG="$CONTAINER_DIR/rbbt.singularity.img"
|
|
185
|
-
|
|
186
|
-
rsync -avz "$SINGULARITY_OVERLAY_DIR"/ "$CONTAINER_DIR/rbbt.singularity.overlays/" 1>&2
|
|
187
|
-
SINGULARITY_OVERLAY_DIR="$CONTAINER_DIR/rbbt.singularity.overlays"
|
|
188
185
|
EOF
|
|
189
186
|
end
|
|
190
187
|
|
|
@@ -206,11 +203,10 @@ EOF
|
|
|
206
203
|
exec_cmd = %(env _JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m")
|
|
207
204
|
|
|
208
205
|
if singularity
|
|
209
|
-
singularity_exec = %(singularity exec -e
|
|
206
|
+
singularity_exec = %(singularity exec -e -B $SINGULARITY_OPT:/singularity_opt/ -B /apps/)
|
|
210
207
|
|
|
211
208
|
if contain
|
|
212
209
|
singularity_exec << %( -C -H "$CONTAINER_DIR" \
|
|
213
|
-
-B /apps/ \
|
|
214
210
|
-B /scratch/tmp \
|
|
215
211
|
-B "$SINGULARITY_RUBY_INLINE":"$CONTAINER_DIR/.ruby_inline":rw \
|
|
216
212
|
-B ~/git:"$CONTAINER_DIR/git":ro \
|
|
@@ -221,7 +217,7 @@ EOF
|
|
|
221
217
|
"$SINGULARITY_IMG")
|
|
222
218
|
exec_cmd << ' TMPDIR="$CONTAINER_DIR/.rbbt/tmp" '
|
|
223
219
|
else
|
|
224
|
-
singularity_exec += %( -B
|
|
220
|
+
singularity_exec += %( -B "$SINGULARITY_RUBY_INLINE":"$HOME/.ruby_inline":rw "$SINGULARITY_IMG" )
|
|
225
221
|
end
|
|
226
222
|
|
|
227
223
|
if development
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-util
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 5.26.
|
|
4
|
+
version: 5.26.44
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2019-07-
|
|
11
|
+
date: 2019-07-25 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: rake
|