1. Login to `transit.uppmax.uu.se`
Documentation:
- https://uppmax.github.io/UPPMAX-documentation/cluster_guides/transfer_bianca/#transit-server
2. Mount the `wharf` of your project.
```bash
user@transit:~$ mount_wharf sens2023531
Mounting wharf (accessible for you only) to /home/<user>/sens2023531
<user>-sens2023531@bianca-sftp.uppmax.uu.se's password:
```
4. Navigate to your `wharf` folder
5. Disable Singularity cache
```bash
export SINGULARITY_DISABLE_CACHE=true
export APPTAINER_DISABLE_CACHE=true
unset NXF_SINGULARITY_CACHEDIR
```
5. Load nf-core software module
```bash
module load uppmax bioinfo-tools nf-core
```
7. Run `nf-core` to download the pipeline.
```bash
nf-core download pixelator
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.1 - https://nf-co.re
WARNING Could not find GitHub authentication token. Some API requests may fail.
? Select release / branch: 1.0.2 [release]
? Include the nf-core's default institutional configuration files into the download? Yes
In addition to the pipeline code, this tool can download software containers.
? Download software container images: singularity
Nextflow and nf-core can use an environment variable called $NXF_SINGULARITY_CACHEDIR that is a path to a directory where remote
Singularity images are stored. This allows downloaded images to be cached in a central location.
? Define $NXF_SINGULARITY_CACHEDIR for a shared Singularity image download folder? [y/n]: n
If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file.
This is not recommended when downloading Singularity images, as it can take a long time and saves very little space.
? Choose compression type: none
INFO Saving 'nf-core/pixelator'
Pipeline revision: '1.0.2'
Use containers: 'singularity'
Container library: 'quay.io'
Output directory: 'nf-core-pixelator_1.0.2'
Include default institutional configuration: 'True'
INFO Downloading centralised configs from GitHub
INFO Downloading workflow files from GitHub
INFO Processing workflow revision 1.0.2, found 4 container images in total.
Downloading singularity images ???????????????????????????????????????????????????????????????????????????????? 100% ? 4/4 completed
```
8. Running on Bianca
```bash
module load bioinfo-tools Nextflow
nextflow run ... -profile uppmax --project sens-XXXX-XX ....
```
Note: you might need `-c configs/conf/uppmax.config`, make sure you have the file (it is an option to download it during the pipeline download process).
https://github.com/nf-core/configs/blob/master/conf/uppmax.config
https://nf-co.re/configs/uppmax
## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)
###### tags: `UPPMAX`