From 5a9dbe5d7c5472f3001f5c860ce498b97b073ce4 Mon Sep 17 00:00:00 2001 From: phue Date: Mon, 28 Oct 2019 14:11:34 +0100 Subject: [PATCH 1/4] MENDEL is no more the cluster is no longer operational, was replaced by CBE --- README.md | 1 - conf/mendel.config | 24 ------------------------ docs/mendel.md | 18 ------------------ nfcore_custom.config | 1 - 4 files changed, 44 deletions(-) delete mode 100644 conf/mendel.config delete mode 100644 docs/mendel.md diff --git a/README.md b/README.md index 451c12f..20fafd7 100644 --- a/README.md +++ b/README.md @@ -95,7 +95,6 @@ Currently documentation is available for the following clusters: * [GIS](docs/gis.md) * [HEBBE](docs/hebbe.md) * [KRAKEN](docs/kraken.md) -* [MENDEL](docs/mendel.md) * [MUNIN](docs/munin.md) * [PASTEUR](docs/pasteur.md) * [PHOENIX](docs/phoenix.md) diff --git a/conf/mendel.config b/conf/mendel.config deleted file mode 100644 index 0fb7e81..0000000 --- a/conf/mendel.config +++ /dev/null @@ -1,24 +0,0 @@ -//Profile config names for nf-core/configs -params { - config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs' - config_profile_contact = 'Patrick Hüther (@phue)' - config_profile_url = 'http://www.gmi.oeaw.ac.at/' -} - -manifest { - nextflowVersion = '>=19.01.0' -} - -process { - beforeScript = 'module load Miniconda3/4.6.7' - executor = 'pbspro' - clusterOptions = { "-P $params.project" } -} - -params { - max_cpus = 32 - max_memory = 128.GB - max_time = 192.h - igenomes_ignore = true - igenomesIgnore = true //deprecated -} diff --git a/docs/mendel.md b/docs/mendel.md deleted file mode 100644 index ae0ad4c..0000000 --- a/docs/mendel.md +++ /dev/null @@ -1,18 +0,0 @@ -# nf-core/configs: MENDEL Configuration - -All nf-core pipelines have been successfully configured for use on the MENDEL CLUSTER at the Gregor Mendel Institute (GMI). - -To use, run the pipeline with `-profile conda,mendel`. This will download and launch the [`mendel.config`](../conf/mendel.config) which has been pre-configured with a setup suitable for the MENDEL cluster. A Conda environment will be created automatically and software dependencies will be resolved via [bioconda](https://bioconda.github.io/). - -Before running the pipeline you will need to load Conda using the environment module system on MENDEL. You can do this by issuing the commands below: - -```bash -## Load Nextflow and Conda environment modules -module purge -module load Nextflow -module load Miniconda/4.6.7 -``` - ->NB: You will need an account to use the HPC cluster in order to run the pipeline. If in doubt contact the HPC team. - ->NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact the HPC team. diff --git a/nfcore_custom.config b/nfcore_custom.config index 06182f5..12a0c1e 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -25,7 +25,6 @@ profiles { gis { includeConfig "${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" } - mendel { includeConfig "${params.custom_config_base}/conf/mendel.config" } munin { includeConfig "${params.custom_config_base}/conf/munin.config" } pasteur { includeConfig "${params.custom_config_base}/conf/pasteur.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } From 47a7d57db4c7d2acec49f468d69eb340286d1d4c Mon Sep 17 00:00:00 2001 From: maxibor Date: Mon, 28 Oct 2019 16:09:00 +0100 Subject: [PATCH 2/4] update shh doc --- docs/shh.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/shh.md b/docs/shh.md index 67cf3b9..aff3f21 100644 --- a/docs/shh.md +++ b/docs/shh.md @@ -10,7 +10,8 @@ To use, run the pipeline with `-profile shh`. This will download and launch the however this will likely change to a read-only directory in the future that will be managed by IT. -Note that **the configuration file is currently optimised for `nf-core/eager`**. It will submit to the short queue but with a walltime of 2 hours. +This configuration will automatically choose the correct SLURM queue (`short`,`medium`,`long`,`supercruncher`) depending on the time and memory required by each process. +Please note that there is no `supercruncher` queue on CDAG. >NB: You will need an account and VPN access to use the cluster at MPI-SHH in order to run the pipeline. If in doubt contact IT. From 99f4d9b9bd1bdd7465e9453c0ff209654a0ed8a0 Mon Sep 17 00:00:00 2001 From: arontommi Date: Wed, 6 Nov 2019 13:10:09 +0100 Subject: [PATCH 3/4] documentation on how to fix bianca cluster configuration problem --- docs/uppmax.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docs/uppmax.md b/docs/uppmax.md index 07a7f14..d5bba37 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -26,6 +26,12 @@ If running on Bianca, you will have no internet connection and these configs wil Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca. This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available. +Please note that Bianca only allocates 7 GB memory per core so max memory needs to be configured: + +```bash +--max_memory "112GB" +``` + ## Getting more memory If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags: From 5e7d13df89b45932cdc054fd1123d57c49f12dc1 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 8 Nov 2019 10:59:34 +0100 Subject: [PATCH 4/4] Update uppmax.md --- docs/uppmax.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/uppmax.md b/docs/uppmax.md index d5bba37..61a1832 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -26,7 +26,7 @@ If running on Bianca, you will have no internet connection and these configs wil Please use the nf-core helper tool on a different system to download the required pipeline files, and transfer them to bianca. This helper tool bundles the config files in this repo together with the pipeline files, so the profile will still be available. -Please note that Bianca only allocates 7 GB memory per core so max memory needs to be configured: +Note that Bianca only allocates 7 GB memory per core so the max memory needs to be limited: ```bash --max_memory "112GB"