From 1d23ba9264f19aa7b29c33492c02ef11c41c9637 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85shild=20J=2E=20V=C3=A5gene?= <60298098+ashildv@users.noreply.github.com> Date: Thu, 2 Jun 2022 16:40:29 +0200 Subject: [PATCH] change name of tmp dir to .tmp_nfcore --- docs/mjolnir_globe.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/mjolnir_globe.md b/docs/mjolnir_globe.md index 3f6beaf..f22fffd 100644 --- a/docs/mjolnir_globe.md +++ b/docs/mjolnir_globe.md @@ -2,24 +2,24 @@ > **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT. -Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_eager` in their data/project directory on Mjolnir where the temp files from `nf-core/eager` will be re-directed by the `NXF_TEMP` command (see below). +Prior to running the pipeline for the first time with the `mjolnir_globe.config` (../conf/mjolnir_globe.config), users **must** create a hidden directory called `.tmp_nfcore` in their data/project directory on Mjolnir where the temp files from nf-core pipelines will be re-directed by the `NXF_TEMP` command (see below). -The contents of the `.tmp_eager` directory should be periodically deleted manually to save on space. +The contents of the `.tmp_nfcore` directory should be periodically deleted manually to save on space. If the `NXF_TEMP` command is not used to properly re-direct temp files the `/tmp` directory on the compute nodes will be used and quickly filled up, which blocks anyone from working on these nodes until the offending user removes their files. The following lines **must** be added by users to their `~/.bash_profile`: ```bash #re-direct tmp files away from /tmp directories on compute nodes or the headnode -export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_eager +export NXF_TEMP=/maps/projects/mjolnir1/people/$USER/.tmp_nfcore # nextflow - limiting memory of virtual java machine NXF_OPTS='-Xms1g -Xmx4g' ``` -Once you have created the `.tmp_eager` directory and added the above lines of code to your `.bash_profile` you can run the pipeline. +Once you have created the `.tmp_nfcore` directory and added the above lines of code to your `.bash_profile` you can run an nf-core pipeline. -Before running the pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: +Before running a pipeline you will need to load Java, Miniconda, Singularity and Nextflow. You can do this by including the commands below in your SLURM/sbatch script: ```bash ## Load Java and Nextflow environment modules