From afc699dd56a9ba65ac1a0f5aa2fc1292bfbe3ec3 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Mon, 15 Jan 2024 15:00:25 +0100 Subject: [PATCH 1/9] increase memory --- files/galaxy/tpv/tools.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index e13a2313f..fc43e4ae1 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -733,6 +733,10 @@ tools: - if: input_size >= 25 fail: Too much data, please check if the input is correct. + toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: + cores: 10 + mem: 80 + toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers cores: 10 From 5c642397d20e91f8a68e62b7c7d3d5ce72853d89 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 31 Jan 2024 15:06:17 +0100 Subject: [PATCH 2/9] increase only for assembly --- files/galaxy/tpv/tools.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index fc43e4ae1..6b85bccee 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -734,8 +734,11 @@ tools: fail: Too much data, please check if the input is correct. toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: - cores: 10 - mem: 80 + rules: + - if: | + helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + cores: 20 + mem: 80 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers From a236b9f3fc22086ccac2b8ee4ddd7a72d3dc5675 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 31 Jan 2024 15:12:43 +0100 Subject: [PATCH 3/9] linting --- files/galaxy/tpv/tools.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 6b85bccee..494548d5c 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -735,8 +735,7 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: rules: - - if: | - helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + - if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) cores: 20 mem: 80 From 28febb1c0ec43faaf57babdba3cd49a650172140 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 31 Jan 2024 15:15:37 +0100 Subject: [PATCH 4/9] linting --- files/galaxy/tpv/tools.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 494548d5c..ff69fab6d 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -735,7 +735,8 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: rules: - - if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + if: | + helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) cores: 20 mem: 80 From cb1672c290bce9ec759535091e4bf82aae7cb937 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 31 Jan 2024 15:18:44 +0100 Subject: [PATCH 5/9] linting --- files/galaxy/tpv/tools.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index ff69fab6d..384c1eb8f 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -734,11 +734,11 @@ tools: fail: Too much data, please check if the input is correct. toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: - rules: - if: | - helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) - cores: 20 - mem: 80 + rules: + if: | + helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + cores: 20 + mem: 80 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers From 30d3687f1afd641f6d7c92ad1235971ba2d05918 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 31 Jan 2024 21:07:12 +0100 Subject: [PATCH 6/9] Update tools.yml --- 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 384c1eb8f..05589e2fa 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -735,8 +735,8 @@ tools: toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: rules: - if: | - helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + - id: metagenome + if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) cores: 20 mem: 80 From 56915aa9a5f372959f0e351ec4a8e0aa68ae43f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 31 Jan 2024 21:08:23 +0100 Subject: [PATCH 7/9] Update tools.yml --- files/galaxy/tpv/tools.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 05589e2fa..7cdcc9447 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -734,6 +734,8 @@ tools: fail: Too much data, please check if the input is correct. toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/.*: + cores: 10 + mem: 12 rules: - id: metagenome if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) From 280922efc581f5359dea6c368527cf62e0e412fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Wed, 31 Jan 2024 21:11:54 +0100 Subject: [PATCH 8/9] Update tools.yml --- files/galaxy/tpv/tools.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 7cdcc9447..15c612565 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -737,10 +737,10 @@ tools: cores: 10 mem: 12 rules: - - id: metagenome - if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) - cores: 20 - mem: 80 + - id: metagenome + if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + cores: 20 + mem: 80 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/.*: # see https://github.com/usegalaxy-eu/infrastructure-playbook/pull/881 for some numbers From 8f1a1ef8b69e8f5a21b8e2428b050678b0199a14 Mon Sep 17 00:00:00 2001 From: Sanjay Kumar Srikakulam Date: Thu, 1 Feb 2024 16:59:30 +0100 Subject: [PATCH 9/9] Fix YAML nested mappings --- files/galaxy/tpv/tools.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml index 15c612565..66c462cdf 100644 --- a/files/galaxy/tpv/tools.yml +++ b/files/galaxy/tpv/tools.yml @@ -738,7 +738,8 @@ tools: mem: 12 rules: - id: metagenome - if: helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) + if: | + helpers.job_args_match(job, app, {'assembly': {'type': 'Metagenome'}}) cores: 20 mem: 80