From a5ef109170d40b3beb4ee88bffef4a078f94b734 Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Tue, 26 Nov 2024 14:20:58 -0500 Subject: [PATCH 1/3] Add requirements for the Galaxy-ME tools --- tools.yml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/tools.yml b/tools.yml index 3a44773..9874973 100644 --- a/tools.yml +++ b/tools.yml @@ -2681,6 +2681,36 @@ tools: mem: 19.0 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/.*: mem: 22.8 + toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/.*: + cores: 8 + mem: 64 + toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/.*: + cores: 12 + mem: 128 + toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/.*: + cores: 8 + mem: 64 + toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/.*: + cores: 24 + mem: 478 + toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/.*: + cores: 12 + mem: 128 + toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/.*: + cores: 8 + mem: 64 + toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/.*: + cores: 1 + mem: 2 + toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/.*: + cores: 4 + mem: 16 + toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/.*: + cores: 4 + mem: 16 + toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*: + cores: 8 + mem: 64 .*bowtie2_index_builder_data_manager.*: cores: 16 .*bwa_mem_index_builder_data_manager.*: From 66293c038f60430442aae763117cd96330048ba8 Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Tue, 26 Nov 2024 14:33:41 -0500 Subject: [PATCH 2/3] Format --- tools.yml | 60 +++++++++++++++++++++++++++---------------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/tools.yml b/tools.yml index 9874973..7bb5bef 100644 --- a/tools.yml +++ b/tools.yml @@ -1118,12 +1118,30 @@ tools: toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*: cores: 16 mem: 61.4 + toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/.*: + cores: 24 + mem: 478 + toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/.*: + cores: 1 + mem: 2 + toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/.*: + cores: 4 + mem: 16 + toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/.*: + cores: 4 + mem: 16 + toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*: + cores: 8 + mem: 64 toolshed.g2.bx.psu.edu/repos/guerler/charts/charts/.*: mem: 10 toolshed.g2.bx.psu.edu/repos/hammock/hammock/hammock_1.0/.*: mem: 20 env: _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G + toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/.*: + cores: 12 + mem: 128 toolshed.g2.bx.psu.edu/repos/imgteam/projective_transformation/ip_projective_transformation/.*: mem: 24 toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/scale_image/.*: @@ -2578,6 +2596,18 @@ tools: mem: 330 toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/.*: mem: 20 + toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/.*: + cores: 12 + mem: 128 + toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/.*: + cores: 8 + mem: 64 + toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/.*: + cores: 8 + mem: 64 + toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/.*: + cores: 8 + mem: 64 toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/.*: mem: 20 toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/.*: @@ -2681,36 +2711,6 @@ tools: mem: 19.0 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/.*: mem: 22.8 - toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/.*: - cores: 8 - mem: 64 - toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/.*: - cores: 12 - mem: 128 - toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/.*: - cores: 8 - mem: 64 - toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/.*: - cores: 24 - mem: 478 - toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/.*: - cores: 12 - mem: 128 - toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/.*: - cores: 8 - mem: 64 - toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/.*: - cores: 1 - mem: 2 - toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/.*: - cores: 4 - mem: 16 - toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/.*: - cores: 4 - mem: 16 - toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*: - cores: 8 - mem: 64 .*bowtie2_index_builder_data_manager.*: cores: 16 .*bwa_mem_index_builder_data_manager.*: From d1ac7ec6f4edd7ea3ce491dce1072c58431501ea Mon Sep 17 00:00:00 2001 From: Enis Afgan Date: Tue, 3 Dec 2024 10:30:51 -0500 Subject: [PATCH 3/3] Set mem for ip_convertimage to 30GB --- tools.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools.yml b/tools.yml index 7bb5bef..b059e53 100644 --- a/tools.yml +++ b/tools.yml @@ -1141,7 +1141,7 @@ tools: _JAVA_OPTIONS: -Xmx{int(mem)}G -Xms1G toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/.*: cores: 12 - mem: 128 + mem: 30 toolshed.g2.bx.psu.edu/repos/imgteam/projective_transformation/ip_projective_transformation/.*: mem: 24 toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/scale_image/.*: