From 51d057564f9fc43248f718a2aff0f710ff3ee8e3 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 15 Jun 2022 15:40:42 +0200 Subject: [PATCH 01/21] Fix python related seg faults mag@eva --- conf/pipeline/mag/eva.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/pipeline/mag/eva.config b/conf/pipeline/mag/eva.config index 81d8d0c..37a531d 100644 --- a/conf/pipeline/mag/eva.config +++ b/conf/pipeline/mag/eva.config @@ -4,6 +4,11 @@ params { config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs' } +env { + OPENBLAS_NUM_THREADS=1 + OMP_NUM_THREADS=1 +} + process { withName: FASTQC { From c479780d8f2e0e802b56c12ff836d11aa223397f Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:38:20 +0000 Subject: [PATCH 02/21] create mana config --- conf/mana.config | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 conf/mana.config diff --git a/conf/mana.config b/conf/mana.config new file mode 100644 index 0000000..47f1992 --- /dev/null +++ b/conf/mana.config @@ -0,0 +1,20 @@ +params { + config_profile_description = 'University of Hawaii at Manoa' + config_profile_url = 'http://www.hawaii.edu/its/ci/' + config_profile_contact = 'Cedric Arisdakessian' + + max_memory = 400.GB + max_cpus = 96 + max_time = 72.h +} + +process { + executor = 'slurm' + queue = 'shared,exclusive,kill-shared,kill-exclusive' + module = 'tools/Singularity' +} + +singularity { + enabled = true + cacheDir = "$HOME/.singularity_images_cache" +} From 32cdea4b59788dedee89fd88e0e4f799fb91cc20 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:38:48 +0000 Subject: [PATCH 03/21] documentation for mana config --- docs/mana.md | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 docs/mana.md diff --git a/docs/mana.md b/docs/mana.md new file mode 100644 index 0000000..030749c --- /dev/null +++ b/docs/mana.md @@ -0,0 +1,46 @@ +# nf-core/configs Mana (at University of Hawaii at Manoa) Configuration + +To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): + +- Load singularity and use it as default container technology +- Setup a container cache directory in your home (~/.singularity_images_cache) +- Select appropriate queues (currently: `shared,exclusive,kill-shared,kill-exclusive`) +- Set the maximum available resources (available in 09/02/2022): + - CPUs: 96 + - Memory: 400.GB + - Time: 72.h + + +## Pre-requisites + +In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment. +At the moment, nextflow is not available as a module (but might be in the future). + +### Install nextflow in a conda environment + +Before we start, we will need to work on an interactive node (currently, mana doesn't let you execute any program in the login node): + +```bash +# Request an interactive sandbox node for 30 min +srun --pty -t 30 -p sandbox /bin/bash +``` + +To setup nextflow on your account, follow these steps. + +```bash +# Load the latest anaconda3 module +module load lang/Anaconda3 + +# Initialize environment +. /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh + +# Install nextflow (here in base environment, but you can create a new one if you'd like) +conda install -c bioconda nextflow +``` + +If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this: + +```bash +echo "module load lang/Anaconda3" >> ~/.bash_profile +echo ". /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh >> ~/.bash_profile" +``` \ No newline at end of file From 9b710a07f54be03cb161fcda83b31c5a407d8d25 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:41:23 +0000 Subject: [PATCH 04/21] add mana config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index aba5349..aec233f 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -52,6 +52,7 @@ profiles { ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"} lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" } maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" } + mana { includeConfig "${params.custom_config_base}/conf/mana.config" } marvin { includeConfig "${params.custom_config_base}/conf/marvin.config" } medair { includeConfig "${params.custom_config_base}/conf/medair.config" } mjolnir_globe { includeConfig "${params.custom_config_base}/conf/mjolnir_globe.config" } From 7b1e360a3588627de30c76431d7a561d39b792da Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:42:07 +0000 Subject: [PATCH 05/21] added mana --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 838d288..e432ec7 100644 --- a/README.md +++ b/README.md @@ -125,6 +125,7 @@ Currently documentation is available for the following systems: - [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) +- [MANA](docs/mana.md) - [MARVIN](docs/marvin.md) - [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) From 9cc679c811bda824f581cacbcdc764ee63b48642 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:43:51 +0000 Subject: [PATCH 06/21] fix mana name --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e432ec7..c476905 100644 --- a/README.md +++ b/README.md @@ -125,7 +125,7 @@ Currently documentation is available for the following systems: - [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) -- [MANA](docs/mana.md) +- [Mana](docs/mana.md) - [MARVIN](docs/marvin.md) - [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) From 3b8b1702030e6e85e1ff147b0b7355de4b7b17f2 Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:47:03 +0000 Subject: [PATCH 07/21] added mana in gh actions --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e4d68ca..16453da 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -69,6 +69,7 @@ jobs: - "jax" - "ku_sund_dangpu" - "lugh" + - "mana" - "marvin" - "medair" - "mjolnir_globe" From e89cb7bd5e6257a8918bbfe427396cab8758c74d Mon Sep 17 00:00:00 2001 From: Cedric Arisdakessian Date: Mon, 3 Oct 2022 03:49:04 +0000 Subject: [PATCH 08/21] fix indentation --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 16453da..c057f2b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -69,7 +69,7 @@ jobs: - "jax" - "ku_sund_dangpu" - "lugh" - - "mana" + - "mana" - "marvin" - "medair" - "mjolnir_globe" From d429a59a0d76207dbff6be8c98984df4138372be Mon Sep 17 00:00:00 2001 From: Cedric Date: Sun, 2 Oct 2022 18:44:22 -1000 Subject: [PATCH 09/21] add automounts for singularity --- conf/mana.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/mana.config b/conf/mana.config index 47f1992..93d674c 100644 --- a/conf/mana.config +++ b/conf/mana.config @@ -17,4 +17,5 @@ process { singularity { enabled = true cacheDir = "$HOME/.singularity_images_cache" + autoMounts = true } From 2825f33ded98415fbd5bac31c6c74a3618b999a9 Mon Sep 17 00:00:00 2001 From: Cedric Date: Sun, 2 Oct 2022 19:15:59 -1000 Subject: [PATCH 10/21] conda env setup improvement --- docs/mana.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/mana.md b/docs/mana.md index 030749c..d3c3230 100644 --- a/docs/mana.md +++ b/docs/mana.md @@ -29,10 +29,10 @@ To setup nextflow on your account, follow these steps. ```bash # Load the latest anaconda3 module -module load lang/Anaconda3 +module load lang/Anaconda3/2022.05 # Initialize environment -. /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh +. $(conda info --base)/etc/profile.d/conda.sh # Install nextflow (here in base environment, but you can create a new one if you'd like) conda install -c bioconda nextflow @@ -41,6 +41,6 @@ conda install -c bioconda nextflow If you want these settings to be persistent, you can add the first 2 commands in your .bash_profile file like this: ```bash -echo "module load lang/Anaconda3" >> ~/.bash_profile -echo ". /opt/apps/software/lang/Anaconda3/5.1.0/etc/profile.d/conda.sh >> ~/.bash_profile" -``` \ No newline at end of file +echo "module load lang/Anaconda3/2022.05" >> ~/.bash_profile +echo "$(conda info --base)/etc/profile.d/conda.sh" >> ~/.bash_profile +``` From ce39096f32d94071a9fdd2aab6e93c3bfaecbe7a Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:44:19 +0200 Subject: [PATCH 11/21] Create tigem.config --- conf/tigem.config | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 conf/tigem.config diff --git a/conf/tigem.config b/conf/tigem.config new file mode 100644 index 0000000..1e5adea --- /dev/null +++ b/conf/tigem.config @@ -0,0 +1,31 @@ +params { + config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.' + config_profile_contact = 'Giuseppe Martone (@giusmar)' + config_profile_url = 'https://github.com/giusmar' +} + +process.executor = 'slurm' +google.zone = 'europe-west1' + +singularity { + enabled = true + autoMounts = true + cacheDir = 'work/singularity' +} + +timeline { + enabled = true + file = "${params.outdir}/execution/timeline.html" +} +report { + enabled = true + file = "${params.outdir}/execution/report.html" +} +trace { + enabled = true + file = "${params.outdir}/execution/trace.txt" +} +dag { + enabled = true + file = "${params.outdir}/execution/pipeline.svg" +} From da0482a904fb3ec4d9d6f92a942db89f79ecc7a4 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:52:50 +0200 Subject: [PATCH 12/21] Create tigem.md --- docs/tigem.md | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 docs/tigem.md diff --git a/docs/tigem.md b/docs/tigem.md new file mode 100644 index 0000000..6997e82 --- /dev/null +++ b/docs/tigem.md @@ -0,0 +1,7 @@ +# nf-core/configs: TIGEM configuration + +To use, run the pipeline with -profile tigem. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. + +--- + +For this pipeline you need a docker container containing the tools needed for the specific pipeline. You can find the docker containers on giusmar docker hub profile. A docker image containing the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. From 2479c1e7e8af9c512d11ea5023d940eb71d18337 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:53:27 +0200 Subject: [PATCH 13/21] Update tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 6997e82..31e42de 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -1,6 +1,6 @@ # nf-core/configs: TIGEM configuration -To use, run the pipeline with -profile tigem. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. +To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster. --- From bde7502ed278e90a3c0b8071ace5f65b0b30d330 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 10:54:13 +0200 Subject: [PATCH 14/21] Update nfcore_custom.config --- nfcore_custom.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nfcore_custom.config b/nfcore_custom.config index aba5349..97b66f2 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -69,6 +69,7 @@ profiles { sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} sbc_sharc { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} + tigem { includeConfig "${params.custom_config_base}/conf/tigem.config"} uct_hpc { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" } unibe_ibu { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } From a4244eb3462475bd90109f06a2cdb8cb03ee1600 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 11:06:26 +0200 Subject: [PATCH 15/21] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 838d288..da1d6f1 100644 --- a/README.md +++ b/README.md @@ -141,6 +141,7 @@ Currently documentation is available for the following systems: - [SANGER](docs/sanger.md) - [SBC_SHARC](docs/sbc_sharc.md) - [SEG_GLOBE](docs/seg_globe.md) +- [TIGEM](docs/tigem.md) - [UCT_HPC](docs/uct_hpc.md) - [UNIBE_IBU](docs/unibe_ibu.md) - [UPPMAX](docs/uppmax.md) From 5758687a091d40271ccda8716e5a2be3743d0afc Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 11:07:36 +0200 Subject: [PATCH 16/21] Update main.yml --- .github/workflows/main.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e4d68ca..61af682 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -87,6 +87,7 @@ jobs: - "sanger" - "sbc_sharc" - "seg_globe" + - "tigem" - "uct_hpc" - "unibe_ibu" - "uppmax" From e5b798e21f157dec8d6cc51a7b705cdc940c1022 Mon Sep 17 00:00:00 2001 From: Marc Hoeppner Date: Tue, 4 Oct 2022 14:07:44 +0200 Subject: [PATCH 17/21] Updating CCGA med to use the new Beegfs file system --- conf/ccga_med.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/ccga_med.config b/conf/ccga_med.config index d55fde2..c9b7b44 100644 --- a/conf/ccga_med.config +++ b/conf/ccga_med.config @@ -13,8 +13,8 @@ params { singularity { enabled = true - runOptions = "-B /work_ifs -B /scratch" - cacheDir = "/work_ifs/ikmb_repository/singularity_cache/" + runOptions = "-B /work_ifs -B /scratch -B /work_beegfs" + cacheDir = "/work_beegfs/ikmb_repository/singularity_cache/" } executor { @@ -31,7 +31,7 @@ process { params { // illumina iGenomes reference file paths on RZCluster - igenomes_base = '/work_ifs/ikmb_repository/references/iGenomes/references/' + igenomes_base = '/work_beegfs/ikmb_repository/references/iGenomes/references/' saveReference = true max_memory = 250.GB max_cpus = 24 From cade84aacd7d533f34c9e52d2abc39c54a290084 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 4 Oct 2022 19:50:51 +0000 Subject: [PATCH 18/21] [automated] Fix linting with Prettier --- docs/mana.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/mana.md b/docs/mana.md index d3c3230..4d0be0d 100644 --- a/docs/mana.md +++ b/docs/mana.md @@ -1,6 +1,6 @@ # nf-core/configs Mana (at University of Hawaii at Manoa) Configuration -To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): +To use, run the pipeline with `-profile mana`. It will use the following parameters for Mana (UHM HPCC): - Load singularity and use it as default container technology - Setup a container cache directory in your home (~/.singularity_images_cache) @@ -10,7 +10,6 @@ To use, run the pipeline with `-profile mana`. It will use the following paramet - Memory: 400.GB - Time: 72.h - ## Pre-requisites In order to run a nf-core pipeline on Mana, you will need to setup nextflow in your environment. From baf857654c60d2fc42dde1601907022a21870047 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 22:28:38 +0200 Subject: [PATCH 19/21] Update tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 31e42de..95d5415 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -4,4 +4,4 @@ To use, run the pipeline with `-profile tigem`. This will download and launch th --- -For this pipeline you need a docker container containing the tools needed for the specific pipeline. You can find the docker containers on giusmar docker hub profile. A docker image containing the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. +This pipeline can be used on TIGEM clusters, in which is installed slurm as job scheduling system, so you can use this config if you have the same tool installed. An additional parameter is google.zone to allow downloading data from GCP for a specific time zone. It should not interfere with a local or an AWS configuration. From e37bccc9d8dff9beff40ae8512b48a0224cd6a00 Mon Sep 17 00:00:00 2001 From: Giuseppe Martone <46596039+giusmar@users.noreply.github.com> Date: Tue, 4 Oct 2022 22:58:50 +0200 Subject: [PATCH 20/21] Update tigem.config --- conf/tigem.config | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/conf/tigem.config b/conf/tigem.config index 1e5adea..b89a4ed 100644 --- a/conf/tigem.config +++ b/conf/tigem.config @@ -12,20 +12,3 @@ singularity { autoMounts = true cacheDir = 'work/singularity' } - -timeline { - enabled = true - file = "${params.outdir}/execution/timeline.html" -} -report { - enabled = true - file = "${params.outdir}/execution/report.html" -} -trace { - enabled = true - file = "${params.outdir}/execution/trace.txt" -} -dag { - enabled = true - file = "${params.outdir}/execution/pipeline.svg" -} From e2146b5905a7b2bf44da160c052c944a6d80055b Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 5 Oct 2022 09:59:07 +0200 Subject: [PATCH 21/21] Update docs/tigem.md --- docs/tigem.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/tigem.md b/docs/tigem.md index 95d5415..e562fe4 100644 --- a/docs/tigem.md +++ b/docs/tigem.md @@ -4,4 +4,4 @@ To use, run the pipeline with `-profile tigem`. This will download and launch th --- -This pipeline can be used on TIGEM clusters, in which is installed slurm as job scheduling system, so you can use this config if you have the same tool installed. An additional parameter is google.zone to allow downloading data from GCP for a specific time zone. It should not interfere with a local or an AWS configuration. +This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.