From 85272c0b44b7068c0e6e04fbba6c303583c161be Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 14:01:44 +0200 Subject: [PATCH 1/7] Updated README to correctly list build status. --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5e8d3a1..b41d33f 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,11 @@ +# molgenis-compute + [![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)](http://www.molgenis.org/jenkins/job/molgenis-compute/) -molgenis-compute ================ + +A workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers like + - [Slurm](https://slurm.schedmd.com/) + - [PBS](http://www.adaptivecomputing.com/products/open-source/torque/) (deprecated) + - [SGE/OGS](http://gridscheduler.sourceforge.net/) (deprecated) + See http://www.molgenis.org/wiki/ComputeStart for documentation. From 1ae5d7502bae9289cbac5084ef126254ded20fa6 Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 14:10:59 +0200 Subject: [PATCH 2/7] Updated README to correctly list build status.2 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b41d33f..dd8df68 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # molgenis-compute -[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)](http://www.molgenis.org/jenkins/job/molgenis-compute/) +[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)] ================ A workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers like From 87f4ae14b3fbead0574ecd6cf478e187a84ec34f Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 14:15:42 +0200 Subject: [PATCH 3/7] Updated README to correctly list build status.3 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index dd8df68..397f3f7 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # molgenis-compute -[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)] +[Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute) ================ A workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers like From 83f8aa5c4f5059549bd518578d01035b307f2860 Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 14:30:58 +0200 Subject: [PATCH 4/7] Updated README to correctly list build status.4 --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 397f3f7..ab98124 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,12 @@ # molgenis-compute + [Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute) -================ + +[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)](http://www.molgenis.org/jenkins/job/molgenis-compute/) +[![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=molgenis-compute)](https://molgenis50.gcc.rug.nl/jenkins/job/molgenis-compute/) + +[![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=Build-molgenis-compute-pull-requests&build=66)](https://molgenis50.gcc.rug.nl/jenkins/job/Build-molgenis-compute-pull-requests/66/) A workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers like - [Slurm](https://slurm.schedmd.com/) From ca53240c43adcfcc809498033ccc08115e4df052 Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 14:34:59 +0200 Subject: [PATCH 5/7] Updated README to correctly list build status.5 --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ab98124..c186f9a 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute) -[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute)](http://www.molgenis.org/jenkins/job/molgenis-compute/) +[![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute&.png)](http://www.molgenis.org/jenkins/job/molgenis-compute/) [![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=molgenis-compute)](https://molgenis50.gcc.rug.nl/jenkins/job/molgenis-compute/) [![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=Build-molgenis-compute-pull-requests&build=66)](https://molgenis50.gcc.rug.nl/jenkins/job/Build-molgenis-compute-pull-requests/66/) From e5be1c2ddb5f55251d5447447abf3f31255016bd Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 10 Aug 2017 15:27:47 +0200 Subject: [PATCH 6/7] Updated README to correctly list build status.6 --- README.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/README.md b/README.md index c186f9a..71e267b 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,6 @@ # molgenis-compute - -[Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute) - [![Build Status](http://www.molgenis.org/jenkins/buildStatus/icon?job=molgenis-compute&.png)](http://www.molgenis.org/jenkins/job/molgenis-compute/) -[![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=molgenis-compute)](https://molgenis50.gcc.rug.nl/jenkins/job/molgenis-compute/) - -[![Build Status](https://molgenis50.gcc.rug.nl/jenkins/buildStatus/icon?job=Build-molgenis-compute-pull-requests&build=66)](https://molgenis50.gcc.rug.nl/jenkins/job/Build-molgenis-compute-pull-requests/66/) A workflow management framework for generating/submitting/monitoring Bash scripts on compute clusters managed by schedulers like - [Slurm](https://slurm.schedmd.com/) From 86db7f56424a3338843dcbfd59f1a85725cbac1e Mon Sep 17 00:00:00 2001 From: pneerincx Date: Thu, 21 Nov 2019 01:13:00 +0100 Subject: [PATCH 7/7] Fixed bug caused by missing underscore at start of local variable name in .../templates/slurm/submit.ftl. --- .../src/main/resources/templates/slurm/submit.ftl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/molgenis-compute-core/src/main/resources/templates/slurm/submit.ftl b/molgenis-compute-core/src/main/resources/templates/slurm/submit.ftl index bc45295..aff87d1 100644 --- a/molgenis-compute-core/src/main/resources/templates/slurm/submit.ftl +++ b/molgenis-compute-core/src/main/resources/templates/slurm/submit.ftl @@ -55,7 +55,7 @@ function cancelJobs () { function processJob () { local _jobName="${1}" - local _jobScript="${jobName}.sh" + local _jobScript="${_jobName}.sh" local _submitOptions="${2:-}" # Optional. local _dependencies="${3:-}" # Optional. local _n=1