From d0c27a054d3cb405addb852eb9f7c9e52db2c50d Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Thu, 28 Nov 2024 17:09:51 +0100 Subject: [PATCH 1/5] Adding tpv variable for cooler_cload_tabix tool --- files/galaxy/tpv/tools.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 12a171e67..4555211c2 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -206,6 +206,11 @@ tools: scheduling: prefer: - condor-tpv + + toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*: + env: + - name: HDF5_USE_FILE_LOCKING + value: "FALSE" toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: rules: From ab497c260fac0bfa333babc99a13f139b293a528 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Thu, 28 Nov 2024 17:16:27 +0100 Subject: [PATCH 2/5] Fix linting --- files/galaxy/tpv/tools.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 4555211c2..cb427e277 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -206,11 +206,11 @@ tools: scheduling: prefer: - condor-tpv - + toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*: env: - name: HDF5_USE_FILE_LOCKING - value: "FALSE" + value: "FALSE" toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: rules: From 5a65d853d68fdcafe2f9da10ea0267257bf010af Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Thu, 28 Nov 2024 17:21:41 +0100 Subject: [PATCH 3/5] Fix linting (2) --- files/galaxy/tpv/tools.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index cb427e277..1b7dc98dd 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -209,7 +209,7 @@ tools: toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*: env: - - name: HDF5_USE_FILE_LOCKING + - name: HDF5_USE_FILE_LOCKING value: "FALSE" toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: From 92f577319f64a55dec3d7563d5f15569658ac0de Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Thu, 28 Nov 2024 17:04:26 +0000 Subject: [PATCH 4/5] add HDF5_USE_FILE_LOCKING ENV and set it to false in TPV tool defaults --- files/galaxy/tpv/tool_defaults.yml | 5 ++++- files/galaxy/tpv/tools.yml | 5 ----- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml index 19d3d0b3c..655d5cf59 100644 --- a/files/galaxy/tpv/tool_defaults.yml +++ b/files/galaxy/tpv/tool_defaults.yml @@ -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: HDF5_USE_FILE_LOCKING + value: "FALSE" params: metadata_strategy: "extended" tmp_dir: true diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 1b7dc98dd..12a171e67 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -207,11 +207,6 @@ tools: prefer: - condor-tpv - toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*: - env: - - name: HDF5_USE_FILE_LOCKING - value: "FALSE" - toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*: rules: - if: input_size >= 0.01 From c7af9b33e7f0ad0371d6d15c5bd37d3b301623b6 Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Thu, 28 Nov 2024 17:10:33 +0000 Subject: [PATCH 5/5] Add the singularity ENV SINGULARITYENV_HDF5_USE_FILE_LOCKING to tool default --- files/galaxy/tpv/tool_defaults.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml index 655d5cf59..87e33030a 100644 --- a/files/galaxy/tpv/tool_defaults.yml +++ b/files/galaxy/tpv/tool_defaults.yml @@ -12,6 +12,8 @@ tools: value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952 - name: HDF5_USE_FILE_LOCKING value: "FALSE" + - name: SINGULARITYENV_HDF5_USE_FILE_LOCKING + value: $HDF5_USE_FILE_LOCKING params: metadata_strategy: "extended" tmp_dir: true