From dbfcd7c5e91ad3ec2afe225ef59eff6e820f5f78 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 17 Jun 2020 15:17:22 +0200 Subject: [PATCH 1/4] Rename uct_hex > uct_hpc --- conf/{uct_hex.config => uct_hpc.config} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename conf/{uct_hex.config => uct_hpc.config} (100%) diff --git a/conf/uct_hex.config b/conf/uct_hpc.config similarity index 100% rename from conf/uct_hex.config rename to conf/uct_hpc.config From 53e118210fbea6a3b6166d73cefa626250d8b303 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 17 Jun 2020 15:20:22 +0200 Subject: [PATCH 2/4] Copy over HPC config --- conf/uct_hpc.config | 38 ++++++++++++++++++++++++++++---------- 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/conf/uct_hpc.config b/conf/uct_hpc.config index 6e0bbbe..e7218ba 100644 --- a/conf/uct_hpc.config +++ b/conf/uct_hpc.config @@ -1,23 +1,41 @@ -//Profile config names for nf-core/configs +/* + * ------------------------------------------------- + * HPC cluster config file + * ------------------------------------------------- + * http://www.hpc.uct.ac.za/ + */ + params { - config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.' - config_profile_contact = 'Katie Lennard (@kviljoen)' - config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/' + config_profile_description = 'University of Cape Town High Performance Cluster config file provided by nf-core/configs.' + config_profile_contact = 'Katie Lennard (@kviljoen)' + config_profile_url = 'http://hpc.uct.ac.za/index.php/hpc-cluster/' + + singularity_cache_dir = "/bb/DB/bio/singularity-containers/" + igenomes_base = '/bb/DB/bio/rna-seq/references' + max_memory = 384.GB + max_cpus = 40 + max_time = 1000.h + hpc_queue = 'ada' + hpc_account = '--account cbio' + genome = 'GRCh37' } singularity { enabled = true - cacheDir = "/scratch/DB/bio/singularity-containers" + cacheDir = params.singularity_cache_dir + autoMounts = true } process { + executor = 'slurm' + queue = params.hpc_queue + // Increasing maxRetries, this will overwrite what we have in base.config + maxRetries = 4 + clusterOptions = params.hpc_account stageInMode = 'symlink' stageOutMode = 'rsync' - queue = 'UCTlong' - clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" } } -executor{ - executor = 'pbs' - jobName = { "$task.tag" } +executor { + queueSize = 15 } From 29f5fa6ce40179e361677b7ea740c99547f14a08 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 17 Jun 2020 15:22:42 +0200 Subject: [PATCH 3/4] uct_hpc docs, readme --- README.md | 2 +- docs/uct_hpc.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 docs/uct_hpc.md diff --git a/README.md b/README.md index e5b199c..4dd4e42 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ Currently documentation is available for the following systems: * [PHOENIX](docs/phoenix.md) * [PRINCE](docs/prince.md) * [SHH](docs/shh.md) -* [UCT_HEX](docs/uct_hex.md) +* [UCT_HPC](docs/uct_hpc.md) * [UPPMAX](docs/uppmax.md) * [UTD_GANYMEDE](docs/utd_ganymede.md) * [UZH](docs/uzh.md) diff --git a/docs/uct_hpc.md b/docs/uct_hpc.md new file mode 100644 index 0000000..dd24e3f --- /dev/null +++ b/docs/uct_hpc.md @@ -0,0 +1,5 @@ +# nf-core/configs: UCT HPC config + +University of Cape Town [High Performance Cluster](http://hpc.uct.ac.za/index.php/hpc-cluster/) config. + +For help or more information, please contact Katie Lennard (@kviljoen). From 18a1a319ec5db8cfc7e9f05e2fabdc8ce62079e6 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 17 Jun 2020 15:25:07 +0200 Subject: [PATCH 4/4] More uct_hex references --- .github/workflows/main.yml | 4 ++-- nfcore_custom.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 45fe4bb..019a3ee 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -16,7 +16,7 @@ jobs: needs: test_all_profiles strategy: matrix: - profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'utd_ganymede', 'uzh'] + profile: ['awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh'] steps: - uses: actions/checkout@v1 - name: Install Nextflow @@ -24,7 +24,7 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Check ${{ matrix.profile }} profile - env: + env: SCRATCH: '~' NXF_GLOBAL_CONFIG: awsbatch.config run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} diff --git a/nfcore_custom.config b/nfcore_custom.config index 6349a15..f61d0cb 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -38,7 +38,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" } - uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } + uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } utd_ganymede { includeConfig "${params.custom_config_base}/conf/utd_ganymede.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }