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move java env options to default tool and reduce xms #1354

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move java env options to default tool and reduce xms #1354

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5 changes: 4 additions & 1 deletion files/galaxy/tpv/tool_defaults.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,10 @@ tools:
mem: cores * 3.8
gpus: 0
env:
GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
- name: GALAXY_MEMORY_MB
value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
- name: _JAVA_OPTIONS
value: -Xmx{round(mem*0.9*1024)}m -Xms256m -Duser.home=/data/2/galaxy_db/tmp -Djava.io.tmpdir=$_GALAXY_JOB_TMP_DIR
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Should we also use for home -> $_GALAXY_JOB_TMP_DIR ?

params:
metadata_strategy: "extended"
tmp_dir: true
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51 changes: 0 additions & 51 deletions files/galaxy/tpv/tools.yml
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Expand Up @@ -930,14 +930,7 @@ tools:
scheduling:
prefer:
- condor-tpv
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
rules:
- if: helpers.tool_version_gte(tool, '2.15.1')
# see usegalaxy-eu/issues#473: https://github.com/usegalaxy-eu/issues/issues/473
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

- if: input_size < 0.1
cores: 1
mem: 4
Expand Down Expand Up @@ -1019,8 +1012,6 @@ tools:
inherits: basic_docker_tool
params:
docker_run_extra_arguments: --user 999
env:
_JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G

toolshed.g2.bx.psu.edu/repos/bgruening/diamond/diamond/.*:
cores: 6
Expand Down Expand Up @@ -1093,12 +1084,6 @@ tools:
inherits: basic_numba_tool
toolshed.g2.bx.psu.edu/repos/computational-metabolomics/dimspy_align_samples/dimspy_align_samples/.*:
inherits: basic_numba_tool
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
toolshed.g2.bx.psu.edu/repos/iracooke/msgfplus/msgfplus/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/.*:
rules:
- if: helpers.tool_version_gte(tool, '4.1.5')
Expand All @@ -1109,29 +1094,6 @@ tools:
RM_LIB_PATH: "/data/db/databases/dfam/3.4/"
- if: helpers.tool_version_gte(tool, '4.1.5')
cores: 4
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx17G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/iuc/bbtools_callvariants/bbtools_callvariants/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/.*:
env:
_JAVA_OPTIONS: -Xmx4G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=4G -Xmx120G -Xms4G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=6G -Xmx14G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/.*:
inherits: basic_numba_tool
Expand All @@ -1151,24 +1113,11 @@ tools:
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/.*:
inherits: basic_numba_tool

toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx15G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/.*:
env:
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/.*:
env:
_JAVA_OPTIONS: -Xmx6G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp

toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/.*:
cores: 24
mem: 80
env:
TERM: vt100
_JAVA_OPTIONS: -XX:MaxPermSize=2G -Xmx6G -Xmx{int(mem)}G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp -Duser.home=/data/2/galaxy_db/tmp
scheduling:
accept:
- pulsar
Expand Down
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