From 16fb95d495cfc5174195ed40392400cef957a307 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 13 Dec 2018 14:55:07 +0100 Subject: [PATCH 1/3] add path to containers on UPPMAX --- conf/uppmax-localhost.config | 1 + conf/uppmax-slurm.config | 1 + 2 files changed, 2 insertions(+) diff --git a/conf/uppmax-localhost.config b/conf/uppmax-localhost.config index a1a08827f..de38fb1f4 100644 --- a/conf/uppmax-localhost.config +++ b/conf/uppmax-localhost.config @@ -12,6 +12,7 @@ env { } params { + containerPath = '/sw/data/uppnex/ToolBox/sarek' genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37' singleCPUMem = 8.GB totalMemory = 104.GB // change to 240 on irma diff --git a/conf/uppmax-slurm.config b/conf/uppmax-slurm.config index 9be0393fa..594cdccd7 100644 --- a/conf/uppmax-slurm.config +++ b/conf/uppmax-slurm.config @@ -7,6 +7,7 @@ */ params { + containerPath = '/sw/data/uppnex/ToolBox/sarek' genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37' runTime = 48.h singleCPUMem = 7.GB // for processes that are using more memory but a single CPU only. Use the 'core' queue for these From b519286e9d276d8ebe630741aa0984cc260c0a06 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 13 Dec 2018 14:55:33 +0100 Subject: [PATCH 2/3] update docs on using containers on UPPMAX --- docs/INSTALL_BIANCA.md | 17 +++-------------- docs/INSTALL_RACKHAM.md | 5 +---- 2 files changed, 4 insertions(+), 18 deletions(-) diff --git a/docs/INSTALL_BIANCA.md b/docs/INSTALL_BIANCA.md index 2137a2403..d7ddb71f8 100644 --- a/docs/INSTALL_BIANCA.md +++ b/docs/INSTALL_BIANCA.md @@ -58,10 +58,11 @@ For more information about using Singularity with UPPMAX, follow the [Singularit ## Install Sarek Sarek use Singularity containers to package all the different tools. +All containers are already stored on UPPMAX. -As `bianca` is secure, no direct download is available, so Sarek and the Singularity containers will have to be installed and updated manually. +As `bianca` is secure, no direct download is available, so Sarek will have to be installed and updated manually. -You can either download Sarek and the containers on your computer (you will need Nextflow and Singularity for that) or on `rackham`, make an archive, and send it to `bianca` using `FileZilla` or `sftp` given your preferences. +You can either download Sarek on your computer or on `rackham`, make an archive, and send it to `bianca` using `FileZilla` or `sftp` given your preferences. All Reference files are already stored in `bianca`. @@ -108,18 +109,6 @@ Wrote Sarek-[snapID].tar.gz > put Sarek-[snapID].tar.gz > exit -# To get the containers -# This script will need Singularity and Nextflow installed -# If executed on Rackham: The script needs to be started from an interactive session -# with at least two cores and approximately 3 hours. The scripts will write about -# 12 Gb data to ~/.singularity, so this amount of disk space needs to be available -# in the users home directory on Rackham. -# -> ./scripts/do_all.sh --pull --tag - -# Send the containers to bianca using the same method -# They will be in the containers/ directory as .img files - # The archive will be in the wharf folder in your user home on your bianca project # Connect to bianca diff --git a/docs/INSTALL_RACKHAM.md b/docs/INSTALL_RACKHAM.md index ab79efb4b..8d6101b16 100644 --- a/docs/INSTALL_RACKHAM.md +++ b/docs/INSTALL_RACKHAM.md @@ -13,10 +13,7 @@ The Reference files are already stored in `rackham`. Nextflow will automatically fetch Sarek from GitHub when launched if `SciLifeLab/Sarek` is specified as the workflow name. Sarek use Singularity containers to package all the different tools. - -On `rackham` you do have the possibility to use the automatic pull of the containers. - -You can choose a specific location to store these, otherwise they will be stored in the directory where you're running Sarek. +All containers are already stored on UPPMAX. ## Test Sarek with small dataset and small reference From ccedb34de2455cf6ac3377ec8c2492bc76f8f582 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 13 Dec 2018 14:56:33 +0100 Subject: [PATCH 3/3] update CHANGELOG --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 495fc9fea..78c30dfba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,10 +21,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#678](https://github.com/SciLifeLab/Sarek/pull/678) - Changing VEP to v92 and adjusting CPUs for VEP - [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script - [#671](https://github.com/SciLifeLab/Sarek/pull/671) - publishDir modes are now params -- [#677](https://github.com/SciLifeLab/Sarek/pull/677) - Update docs +- [#677](https://github.com/SciLifeLab/Sarek/pull/677), [#703](https://github.com/SciLifeLab/Sarek/pull/703) - Update docs - [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Update old awsbatch configuration - [#693](https://github.com/SciLifeLab/Sarek/pull/693) - Qualimap bamQC is now ran after mapping and after recalibration for better QC -- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - update FastQC to `0.11.8` +- [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Update FastQC to `0.11.8` ### `Fixed`