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fix: first draft of bianca guide
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MaxUlysse
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174
docs/uppmax.md
174
docs/uppmax.md
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@ -19,7 +19,7 @@ You can do this with the `--project` flag (two hyphens) when launching nextflow.
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nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags
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```
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> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
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$ NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
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Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
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@ -43,7 +43,7 @@ If your nf-core pipeline run is running out of memory, you can run on a fat node
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```
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This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
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Rackham has nodes with 128GB, 256GB and 1TB memory available.
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`Rackham` has nodes with 128GB, 256GB and 1TB memory available.
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Note that each job will still start with the same request as normal, but restarted attempts with larger requests will be able to request greater amounts of memory.
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@ -76,12 +76,172 @@ To use it, submit with `-profile uppmax,devel`.
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## Running on Bianca
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For security reasons, there is no internet access on Bianca so you can't download from or upload files to the cluster directly. Before running a nf-core pipeline on Bianca you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your Bianca project.
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$ :warning: For more information about `bianca`, follow the [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
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$ :warning: For more information, follow the [nf-core guide for running offline](https://nf-co.re/usage/offline) and the [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
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> :warning: For more information about using `Singularity` with UPPMAX, follow the [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
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You can follow the guide for downloading pipelines [for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use). Note that you will have to download the singularity images as well.
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For security reasons, there is no internet access on `bianca` so you can't download from or upload files to the cluster directly.
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Before running a nf-core pipeline on `bianca` you will first have to download the pipeline and singularity images needed elsewhere and transfer them via the wharf area to your own `bianca` project.
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Next transfer the pipeline and the singularity images to your project. Before running the pipeline you will have to indicate to nextflow where the singularity images are located by setting `NXF_SINGULARITY_CACHEDIR` :
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In this guide, we use `rackham` to download and transfer files to wharf, but it can also be done on your own computer.
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If you use `rackham` to download the pipeline and the singularity containers, we recommend using an interactive session (cf [interactive guide](https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/)), which is what we do in the following guide.
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`export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.`
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### Download Nextflow
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You should now be able to run your nf-core pipeline on bianca.
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You can use the UPPMAX provided `module`, but if necessary, you can also download a more recent version.
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```bash
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# Connect to rackham
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$ ssh -X <user>@rackham.uppmax.uu.se
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# Or stay in your terminal
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# Download the nextflow-all bundle
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$ wget https://github.com/nextflow-io/nextflow/releases/download/v<nextflow_version>/nextflow-<nextflow_version>-all
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# Connect to wharf using sftp
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# For FileZilla follow the bianca user guide
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$ sftp <user>-<bianca_project>@bianca-sftp.uppmax.uu.se:<user>-<bianca_project>
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# Transfer nextflow to wharf
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sftp> put nextflow-<nextflow_version>-all .
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# Exit sftp
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$ exit
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# Connect to bianca
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$ ssh -A <user>-<bianca_project>@bianca.uppmax.uu.se
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# Go to your project
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$ cd /castor/project/proj_nobackup
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# Make folder for Nextflow
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$ mkdir tools
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$ mkdir tools/nextflow
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# Move Nextflow from wharf to its directory
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$ mv /castor/project/proj_nobackup/wharf/<user>/<user>-<bianca_project>/nextflow-<nextflow_version>-all /castor/project/proj_nobackup/tools/nextflow
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# Establish permission
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$ chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-<nextflow_version>-all
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# If you want other people to use it
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# Be sure that your group has rights to the directory as well
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$ chown -R .<bianca_project> /castor/project/proj_nobackup/tools/nextflow/nextflow-<nextflow_version>-all
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# Make a link to it
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$ ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-<nextflow_version>-all /castor/project/proj_nobackup/tools/nextflow/nextflow
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# And every time you're launching Nextflow, don't forget to export the following ENV variables
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# Or add them to your .bashrc file
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$ export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
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$ export PATH=${NXF_HOME}:${PATH}
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$ export NXF_TEMP=$SNIC_TMP
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$ export NXF_LAUNCHER=$SNIC_TMP
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$ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-images
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```
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### Download nf-core pipelines
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```bash
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# Connect to rackham
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$ ssh -X <user>@rackham.uppmax.uu.se
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# Or stay in your terminal
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# Open an interactive session (if you are on rackham)
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$ interactive <rackham_project>
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# Install the latest pip version
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$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev --user
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# Download a pipeline (nf-core/rnaseq 3.0) with the singularity images
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$ nf-core download rnaseq -r 3.0 -s -p 10 --compress none
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# Download a pipeline (nf-core/sarek 2.7) with the singularity images
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$ nf-core download sarek -r 2.7 -s -p 10 --compress none
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# Download specific Singularity images
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$ singularity pull --name nfcore-sareksnpeff-2.7.GRCh38.img docker://nfcore/sareksnpeff:2.7.GRCh38
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$ singularity pull --name nfcore-sarekvep-2.7.GRCh38.img docker://nfcore/sarekvep:2.7.GRCh38
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# Move specific Singularity images into nf-core download folder
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$ mv *.img nf-core-sarek-2.7/singularity-images/.
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# Connect to wharf using sftp
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$ sftp <user>-<bianca_project>@bianca-sftp.uppmax.uu.se:<user>-<bianca_project>
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# Transfer rnaseq folder from rackham to wharf
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sftp> put -r nf-core-rnaseq-3.0 .
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[...]
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# Transfer sarek folder from rackham to wharf
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sftp> put -r nf-core-sarek-2.7 .
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[...]
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# The archives will be in the wharf folder in your user home on your bianca project
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# Connect to bianca
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$ ssh -A <user>-<bianca_project>@bianca.uppmax.uu.se
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# Go to your project
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$ cd /castor/project/proj_nobackup
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# Make and go into a nf-core/sarek directory (where you will store all nf-core/sarek versions)
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$ mkdir sarek
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$ cd sarek
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# Copy the tar from wharf to the project
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$ cp /castor/project/proj_nobackup/wharf/<user>/<user>-<bianca_project>/nf-core-sarek-2.7 /castor/project/proj_nobackup/sarek
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# If you want other people to use it,
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# Be sure that your group has rights to the directory as well
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$ chown -R .<bianca_project> nf-core-sarek-2.7
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# Make a symbolic link to the extracted repository
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$ ln -s nf-core-sarek-2.7 default
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```
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The principle is to have every member of your project to be able to use the same nf-core/sarek version at the same time. So every member of the project who wants to use nf-core/sarek will need to do:
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```bash
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# Connect to bianca
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$ ssh -A <user>-<bianca_project>@bianca.uppmax.uu.se
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# Go to your user directory
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$ cd /home/<user>
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# Make a symbolic link to the default nf-core/sarek
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$ ln -s /castor/project/proj_nobackup/sarek/default sarek
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```
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And then nf-core/sarek can be used with:
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```bash
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$ nextflow run ~/sarek -profile uppmax --project <bianca_project> --genome [GENOME ASSEMBLY] ...
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```
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This is an example of how to run sarek with the tool Manta and the genome assembly version GRCh38, which worked on `bianca` 20210416
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```bash
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$ nextflow run ~/sarek -profile uppmax --project <bianca_project> --tools Manta --input <input.tsv>
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```
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## Update nf-core/sarek
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Repeat the same steps as for installing nf-core/sarek, and update the link.
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```bash
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# Connect to bianca (Connect to rackham first if needed)
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$ ssh -A <user>-<bianca_project>@bianca.uppmax.uu.se
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# Go to the sarek directory in your project
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$ cd /castor/project/proj_nobackup/sarek
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# Remove link
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$ rm default
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# Link to new nf-core/sarek version
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$ ln -s nf-core-sarek-2.7 default
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```
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You can for example keep a `default` version that you are sure is working, an make a link for a `testing` or `development`
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