millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

change name of tmp dir to .tmp_nfcore

Browse source
This commit is contained in:
Åshild J. Vågene 2022-06-02 16:40:29 +02:00 committed by GitHub
parent 2b67d3aaab
commit 1d23ba9264
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 5 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

10
docs/mjolnir_globe.md
View file

@ -2,24 +2,24 @@
> **NB:** You will need an account on Mjolnir to run the pipeline. If in doubt contact IT. > **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. 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`: The following lines **must** be added by users to their `~/.bash_profile`:
```bash ```bash
#re-direct tmp files away from /tmp directories on compute nodes or the headnode #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 # nextflow - limiting memory of virtual java machine
NXF_OPTS='-Xms1g -Xmx4g' 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 ```bash
## Load Java and Nextflow environment modules ## Load Java and Nextflow environment modules