From 8340e89768ede246edb3acbef772d04b0f974782 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Apr 2021 17:28:01 +0100 Subject: [PATCH 01/12] nuig.config first commit --- .github/workflows/main.yml | 2 +- README.md | 1 + conf/nuig.conf | 30 ++++++++++++++++++++++++++++++ docs/nuig.md | 0 nfcore_custom.config | 3 ++- 5 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 conf/nuig.conf create mode 100644 docs/nuig.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 65cabe5..dc8d7e1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'nuig', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 6daff2a..9bce2a1 100644 --- a/README.md +++ b/README.md @@ -120,6 +120,7 @@ Currently documentation is available for the following systems: * [KRAKEN](docs/kraken.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) +* [NUIG](docs/nuig.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) diff --git a/conf/nuig.conf b/conf/nuig.conf new file mode 100644 index 0000000..b46946b --- /dev/null +++ b/conf/nuig.conf @@ -0,0 +1,30 @@ +//Profile config names for nf-core/configs + +params { + config_profile_description = 'National University of Ireland, Galway SLURM cluster profile provided by nf-core/configs' + config_profile_contact = 'Barry Digby (@BarryDigby)' + config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md' +} + +singularity { + enabled = true + autoMounts = true + cacheDir = '/data/containers' +} + +process { + beforeScript = 'module load singularity/3.4.1' + containerOptions = '-B /data/' + executor = 'slurm' + queue = { task.cpus > 8 ? 'highmem' : 'normal' } +} + +/* + NUIG SLURM is not configured to use the memory parameter, please do not include + However, the highmem queue has 128GB memory and the normal queue has 64GB. +*/ + +params { + max_time = '120.d' + max_cpus = '16' +} diff --git a/docs/nuig.md b/docs/nuig.md new file mode 100644 index 0000000..e69de29 diff --git a/nfcore_custom.config b/nfcore_custom.config index 9b4fbda..735402b 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -29,7 +29,7 @@ profiles { icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" } ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" } imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" } - imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } + imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" } genotoul { includeConfig "${params.custom_config_base}/conf/genotoul.config" } google { includeConfig "${params.custom_config_base}/conf/google.config" } denbi_qbic { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" } @@ -39,6 +39,7 @@ profiles { kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" } mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } + nuig { includeConfig "${params.custom_config_base}/conf/nuig.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } From aeb0346cce1c1175829e4e7cd91d879ca7fbfdcb Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Apr 2021 20:14:32 +0100 Subject: [PATCH 02/12] . --- conf/nuig.conf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/nuig.conf b/conf/nuig.conf index b46946b..257ef1c 100644 --- a/conf/nuig.conf +++ b/conf/nuig.conf @@ -9,7 +9,7 @@ params { singularity { enabled = true autoMounts = true - cacheDir = '/data/containers' + cacheDir = '/data/bdigby/containers' } process { From 24a4119e4384e13b9771e30f43cbf47830006cf4 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Thu, 29 Apr 2021 14:24:57 +0100 Subject: [PATCH 03/12] memory test --- conf/nuig.conf | 18 ++++++++++-------- docs/nuig.md | 15 +++++++++++++++ 2 files changed, 25 insertions(+), 8 deletions(-) diff --git a/conf/nuig.conf b/conf/nuig.conf index 257ef1c..4280208 100644 --- a/conf/nuig.conf +++ b/conf/nuig.conf @@ -1,7 +1,7 @@ //Profile config names for nf-core/configs params { - config_profile_description = 'National University of Ireland, Galway SLURM cluster profile provided by nf-core/configs' + config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs' config_profile_contact = 'Barry Digby (@BarryDigby)' config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md' } @@ -9,22 +9,24 @@ params { singularity { enabled = true autoMounts = true - cacheDir = '/data/bdigby/containers' + cacheDir = '/data/containers' } process { - beforeScript = 'module load singularity/3.4.1' + beforeScript = """ + module load EasyBuild/3.4.1 + module load Java/1.8.0_144 + module load singularity/3.4.1 + """ + .stripIndent() containerOptions = '-B /data/' executor = 'slurm' queue = { task.cpus > 8 ? 'highmem' : 'normal' } + withName: '*' { memory = null } } -/* - NUIG SLURM is not configured to use the memory parameter, please do not include - However, the highmem queue has 128GB memory and the normal queue has 64GB. -*/ - params { max_time = '120.d' + max_memory = '64.GB' max_cpus = '16' } diff --git a/docs/nuig.md b/docs/nuig.md index e69de29..571cdd2 100644 --- a/docs/nuig.md +++ b/docs/nuig.md @@ -0,0 +1,15 @@ +# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration + +All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/). + +To use, run the pipeline with `-profile nuig`. This will download and launch the [`nuig.config`](../conf/nuig.config) which has been pre-configured with a setup suitable for Lugh. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. + +## Running nextflow on Lugh + +Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below: + +- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) + +* Install Nextflow edge: download the latest source code from Nextflow GitHub [releases](https://github.com/nextflow-io/nextflow/releases). Unpack source code, compile using `make`, add `nextflow` to your `$PATH` when complete. + +One quirk of Lugh that will produce errors unless addressed: Lugh is not configured to take `memory` parameters in pipelines. This means you will have to make a fork of the pipeline, comment out (`//`) all instances of memory in config files (`nextflow.config`, `base.config`, `test.config` ) AND do away with any instances of `toGiga()` in the pipeline. From 04c0da5a2f7370646419a9f52fea74459a00b858 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 27 Jul 2021 17:05:27 +0100 Subject: [PATCH 04/12] nuig confg (lugh) --- .github/workflows/main.yml | 2 +- README.md | 2 +- conf/{nuig.conf => lugh.config} | 6 +++--- docs/lugh.md | 18 ++++++++++++++++++ docs/nuig.md | 15 --------------- nfcore_custom.config | 2 +- 6 files changed, 24 insertions(+), 21 deletions(-) rename conf/{nuig.conf => lugh.config} (84%) create mode 100644 docs/lugh.md delete mode 100644 docs/nuig.md diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index dc8d7e1..e710ce1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'nuig', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'biohpc_gen', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'lugh', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'sanger', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow diff --git a/README.md b/README.md index 9bce2a1..7d5dc2e 100644 --- a/README.md +++ b/README.md @@ -118,9 +118,9 @@ Currently documentation is available for the following systems: * [ICR_DAVROS](docs/icr_davros.md) * [JAX](docs/jax.md) * [KRAKEN](docs/kraken.md) +* [LUGH](docs/lugh.md) * [MPCDF](docs/mpcdf.md) * [MUNIN](docs/munin.md) -* [NUIG](docs/nuig.md) * [OIST](docs/oist.md) * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) diff --git a/conf/nuig.conf b/conf/lugh.config similarity index 84% rename from conf/nuig.conf rename to conf/lugh.config index 4280208..7a69227 100644 --- a/conf/nuig.conf +++ b/conf/lugh.config @@ -3,7 +3,7 @@ params { config_profile_description = 'National University of Ireland, Galway Lugh cluster profile provided by nf-core/configs' config_profile_contact = 'Barry Digby (@BarryDigby)' - config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/nuig.md' + config_profile_url = 'https://github.com/nf-core/configs/blob/master/docs/lugh.md' } singularity { @@ -17,12 +17,12 @@ process { module load EasyBuild/3.4.1 module load Java/1.8.0_144 module load singularity/3.4.1 + ulimit -s unlimited """ .stripIndent() containerOptions = '-B /data/' executor = 'slurm' - queue = { task.cpus > 8 ? 'highmem' : 'normal' } - withName: '*' { memory = null } + queue = { task.memory >= 64.GB || task.cpus > 16 ? 'highmem' : 'normal' } } params { diff --git a/docs/lugh.md b/docs/lugh.md new file mode 100644 index 0000000..d61ccc3 --- /dev/null +++ b/docs/lugh.md @@ -0,0 +1,18 @@ +# nf-core/configs: LUGH configuration + +To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command. Please take care to use the `-bg` flag or run the job on a compute node. DO NOT RUN ANALYSES ON THE HEAD NODE. + +The configuration file will load prerequisite modules for users, however it is entirely up to the user to have a functional version of nextflow installed in their path. + +Lugh has 3 queues: + + * `MSC`: compute0{1..3}, 16 cpus, 32GB memory (Please reserve for MSc students only) + * `normal`: compute{10..29}, 16 cpus, 64GB memory. + & `highmem`: compute0{4..9}, 32 cpus, 128GB memory. + +The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. Else, `normal`. + +Whilst I (@BarryDigby) am happy to help people set up their nextflow pipelines, please note that I am not the system administrator. + +### Container Cache +Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users. diff --git a/docs/nuig.md b/docs/nuig.md deleted file mode 100644 index 571cdd2..0000000 --- a/docs/nuig.md +++ /dev/null @@ -1,15 +0,0 @@ -# nf-core/configs: National University of Ireland, Galway (Lugh) Configuration - -All nf-core pipelines have been successfully configured for use on Lugh at the [National University of Ireland, Galway](http://maths.nuigalway.ie/biocluster/). - -To use, run the pipeline with `-profile nuig`. This will download and launch the [`nuig.config`](../conf/nuig.config) which has been pre-configured with a setup suitable for Lugh. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. - -## Running nextflow on Lugh - -Before running a pipeline you will need a working version of nextflow. Please follow the install instructions below: - -- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#) - -* Install Nextflow edge: download the latest source code from Nextflow GitHub [releases](https://github.com/nextflow-io/nextflow/releases). Unpack source code, compile using `make`, add `nextflow` to your `$PATH` when complete. - -One quirk of Lugh that will produce errors unless addressed: Lugh is not configured to take `memory` parameters in pipelines. This means you will have to make a fork of the pipeline, comment out (`//`) all instances of memory in config files (`nextflow.config`, `base.config`, `test.config` ) AND do away with any instances of `toGiga()` in the pipeline. diff --git a/nfcore_custom.config b/nfcore_custom.config index 735402b..d835c72 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -37,9 +37,9 @@ profiles { gis { includeConfig "${params.custom_config_base}/conf/gis.config" } hebbe { includeConfig "${params.custom_config_base}/conf/hebbe.config" } kraken { includeConfig "${params.custom_config_base}/conf/kraken.config" } + lugh { includeConfig "${params.custom_config_base}/conf/lugh.config"} mpcdf { includeConfig "${params.custom_config_base}/conf/mpcdf.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } - nuig { includeConfig "${params.custom_config_base}/conf/nuig.config" } oist { includeConfig "${params.custom_config_base}/conf/oist.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } From 4f962260d0bf2f683675582d88a109e71b435637 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 27 Jul 2021 17:08:53 +0100 Subject: [PATCH 05/12] s --- conf/lugh.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/lugh.config b/conf/lugh.config index 7a69227..a6f681b 100644 --- a/conf/lugh.config +++ b/conf/lugh.config @@ -27,6 +27,6 @@ process { params { max_time = '120.d' - max_memory = '64.GB' - max_cpus = '16' + max_memory = '128.GB' + max_cpus = '32' } From 2a06d956b3117a84f5e390ba39beeb3b0f80a3bd Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 27 Jul 2021 17:18:42 +0100 Subject: [PATCH 06/12] mdlint so picky : ( --- docs/lugh.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/lugh.md b/docs/lugh.md index d61ccc3..e89a80a 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -14,5 +14,6 @@ The configuration profile design is very simple. If your process exceeds 64GB me Whilst I (@BarryDigby) am happy to help people set up their nextflow pipelines, please note that I am not the system administrator. -### Container Cache -Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users. +## Container Cache + +Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users. From 70b2644c9a23e629d45d83ab8815f05ab0efefa1 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 27 Jul 2021 17:39:37 +0100 Subject: [PATCH 07/12] . --- conf/lugh.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/lugh.config b/conf/lugh.config index a6f681b..ef80931 100644 --- a/conf/lugh.config +++ b/conf/lugh.config @@ -26,7 +26,7 @@ process { } params { - max_time = '120.d' - max_memory = '128.GB' - max_cpus = '32' + max_time = 120.h + max_memory = 128.GB + max_cpus = 32 } From 380adf083ad0ec8bcb2de0c585449fbe17edfef4 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Jul 2021 11:41:16 +0100 Subject: [PATCH 08/12] markdowwwwn --- docs/lugh.md | 36 +++++++++++++++++++++++++++--------- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/docs/lugh.md b/docs/lugh.md index e89a80a..0a17272 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -1,19 +1,37 @@ # nf-core/configs: LUGH configuration -To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command. Please take care to use the `-bg` flag or run the job on a compute node. DO NOT RUN ANALYSES ON THE HEAD NODE. +Author: Barry Digby +Contact Info: barry.digby@nuigalway.ie +System Administrator: Chris Duke -The configuration file will load prerequisite modules for users, however it is entirely up to the user to have a functional version of nextflow installed in their path. +## Quick Start -Lugh has 3 queues: +To use the lugh configuration profile with your pipeline, add `-profile lugh` to your `nextflow run` command: - * `MSC`: compute0{1..3}, 16 cpus, 32GB memory (Please reserve for MSc students only) - * `normal`: compute{10..29}, 16 cpus, 64GB memory. - & `highmem`: compute0{4..9}, 32 cpus, 128GB memory. +```console +nextflow -bg run nf-core/rnaseq -profile test,nuig +``` -The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. Else, `normal`. +Please take care to use the `-bg` flag, or run the job on a compute node. -Whilst I (@BarryDigby) am happy to help people set up their nextflow pipelines, please note that I am not the system administrator. +:warning: DO NOT RUN ANALYSES ON THE HEAD NODE :warning: + +The configuration file will load prerequisite modules for users (`Java` & `Singularity`), however it is up to the user to have a functional version of `nextflow` installed in their path. Follow `nextflow` installation instructions at the following (link)[https://www.nextflow.io/docs/latest/getstarted.html#installation]. + +## Queue Resources + +| Queue | Hostnames | Max Memory | Max CPUS | Max Time | +|--------- |---------------- |------------ |---------- |---------- | +| MSC | compute[01-03] | 32GB | 16 | 336.h | +| Normal | compute[10-29] | 64GB | 16 | 240.h | +| Highmem | compute[04-09] | 128GB | 32 | 2880.h | + +*** + +The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. If not, it is sent to the `normal` queue. Please do not use the `MSC` queue, this is reserved for Masters students. + +Take others into consideration when deploying your workflow (do not hog the cluster :pig:). If you need to hammer the cluster with a pipeline, please reach out to me and we can tweak the configuration profile to dispatch jobs to only a handful of compute nodes via hostnames. ## Container Cache -Your workflow containers will be downloaded and stored at `/data/containers` which is accessible to all users. +Your workflow containers are stored under `/data/containers/` which is accessible to all users on lugh. From 11cb6cc70dd2885fda9e6d52a9a937ecced38a70 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Jul 2021 11:41:42 +0100 Subject: [PATCH 09/12] w --- docs/lugh.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/lugh.md b/docs/lugh.md index 0a17272..52c9cf9 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -16,7 +16,7 @@ Please take care to use the `-bg` flag, or run the job on a compute node. :warning: DO NOT RUN ANALYSES ON THE HEAD NODE :warning: -The configuration file will load prerequisite modules for users (`Java` & `Singularity`), however it is up to the user to have a functional version of `nextflow` installed in their path. Follow `nextflow` installation instructions at the following (link)[https://www.nextflow.io/docs/latest/getstarted.html#installation]. +The configuration file will load prerequisite modules for users (`Java` & `Singularity`), however it is up to the user to have a functional version of `nextflow` installed in their path. Follow `nextflow` installation instructions at the following [link](https://www.nextflow.io/docs/latest/getstarted.html#installation). ## Queue Resources @@ -30,7 +30,7 @@ The configuration file will load prerequisite modules for users (`Java` & `Singu The configuration profile design is very simple. If your process exceeds 64GB memory or 16 cpus, it is sent to the `highmem` queue. If not, it is sent to the `normal` queue. Please do not use the `MSC` queue, this is reserved for Masters students. -Take others into consideration when deploying your workflow (do not hog the cluster :pig:). If you need to hammer the cluster with a pipeline, please reach out to me and we can tweak the configuration profile to dispatch jobs to only a handful of compute nodes via hostnames. +Take others into consideration when deploying your workflow (do not hog the cluster :pig:). If you need to hammer the cluster with a pipeline, please reach out to me and we can tweak the configuration profile to dispatch jobs to only a handful of compute nodes via hostnames. ## Container Cache From 2fc8082aad5476d5d924a3a56eda445806b24201 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Jul 2021 11:43:39 +0100 Subject: [PATCH 10/12] w --- docs/lugh.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/lugh.md b/docs/lugh.md index 52c9cf9..91dcfdf 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -1,8 +1,6 @@ # nf-core/configs: LUGH configuration -Author: Barry Digby -Contact Info: barry.digby@nuigalway.ie -System Administrator: Chris Duke +
Author: Barry Digby Contact Info: barry.digby@nuigalway.ie System Administrator: Chris Duke
## Quick Start From f62298d211f62b7c1a3985607ed5d23946a21db0 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Jul 2021 11:44:06 +0100 Subject: [PATCH 11/12] w --- docs/lugh.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/lugh.md b/docs/lugh.md index 91dcfdf..cdd3a8c 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -1,6 +1,10 @@ # nf-core/configs: LUGH configuration -
Author: Barry Digby Contact Info: barry.digby@nuigalway.ie System Administrator: Chris Duke
+Author: Barry Digby + +Contact Info: barry.digby@nuigalway.ie + +System Administrator: Chris Duke ## Quick Start From ef6b13e377139bdb2cf03230badc058b4f39d816 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 28 Jul 2021 12:19:11 +0100 Subject: [PATCH 12/12] tabs rm --- docs/lugh.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/lugh.md b/docs/lugh.md index cdd3a8c..567071f 100644 --- a/docs/lugh.md +++ b/docs/lugh.md @@ -22,11 +22,11 @@ The configuration file will load prerequisite modules for users (`Java` & `Singu ## Queue Resources -| Queue | Hostnames | Max Memory | Max CPUS | Max Time | -|--------- |---------------- |------------ |---------- |---------- | -| MSC | compute[01-03] | 32GB | 16 | 336.h | -| Normal | compute[10-29] | 64GB | 16 | 240.h | -| Highmem | compute[04-09] | 128GB | 32 | 2880.h | +| Queue | Hostnames | Max Memory | Max CPUS | Max Time | +|---------|----------------|------------|----------|----------| +| MSC | compute[01-03] | 32GB | 16 | 336.h | +| Normal | compute[10-29] | 64GB | 16 | 240.h | +| Highmem | compute[04-09] | 128GB | 32 | 2880.h | ***