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Merge pull request #201 from maxulysse/master_uppmax_offline

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Improve offline docs for Bianca
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@ -8,42 +8,47 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
## Using the UPPMAX config profile
Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
To use, run the pipeline with `-profile uppmax` (one hyphen).
This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images.
Images for some `nf-core` pipelines are available under `/sw/data/ToolBox/nf-core/` and those can be used by `NXF_SINGULARITY_CACHEDIR=/sw/data/ToolBox/nf-core/; export NXF_SINGULARITY_CACHEDIR`.
In addition to this config profile, you will also need to specify an UPPMAX project id.
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:
You can do this with the `--project` flag (two hyphens) when launching `Nextflow`.
For example:
```bash
nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags
# Launch a nf-core pipeline with the uppmax profile for the project id snic2018-1-234
$ nextflow run nf-core/<PIPELINE> -profile uppmax --project snic2018-1-234 [...]
```
> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
Before running the pipeline you will need to either install Nextflow or load it using the environment module system.
Just run `Nextflow` on a login node and it will handle everything else.
This config enables Nextflow to manage the pipeline jobs via the Slurm job scheduler and using Singularity for software management.
Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
Alternatively, you can also launch `Nextflow` in a `screen` or a `tmux` session.
Just run Nextflow on a login node and it will handle everything else.
## Using AWS iGenomes references
Remember to use `-bg` to launch Nextflow in the background, so that the pipeline doesn't exit if you leave your terminal session.
## Using iGenomes references
A local copy of the iGenomes resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `igenomes.config`.
A local copy of the `AWS iGenomes` resource has been made available on all UPPMAX clusters so you should be able to run the pipeline against any reference available in the `conf/igenomes.config`.
You can do this by simply using the `--genome <GENOME_ID>` parameter.
## Getting more memory
If your nf-core pipeline run is running out of memory, you can run on a fat node with more memory using the following nextflow flags:
If your `nf-core` pipeline run is running out of memory, you can run on a fat node with more memory using the following `Nextflow` flags:
```bash
--clusterOptions "-C mem256GB" --max_memory "256GB"
--clusterOptions "-C mem256GB -p node" --max_memory "256GB"
```
This raises the ceiling of available memory from the default of `128.GB` to `256.GB`.
Rackham has nodes with 128GB, 256GB and 1TB memory available.
`rackham` has nodes with 128GB, 256GB and 1TB memory available.
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.
@ -53,15 +58,15 @@ All jobs will be submitted to fat nodes using this method, so it's only for use
The UPPMAX nf-core configuration profile uses the `hostname` of the active environment to automatically apply the following resource limits:
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
* `bianca`
* cpus available: 16 cpus
* memory available: 109 GB
* `irma`
* cpus available: 16 cpus
* memory available: 250 GB
* `rackham`
* cpus available: 20 cpus
* memory available: 125 GB
## Development config
@ -74,14 +79,197 @@ It is not suitable for use with real data.
To use it, submit with `-profile uppmax,devel`.
## Running on Bianca
## Running on bianca
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.
> :warning: For more information, please follow the following guides:
>
> * [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
> * [nf-core guide for running offline](https://nf-co.re/usage/offline)
> * [nf-core `tools` guide for downloading pipelines for offline use](https://nf-co.re/tools#downloading-pipelines-for-offline-use).
> * [UPPMAX `Singularity` guide](https://www.uppmax.uu.se/support-sv/user-guides/singularity-user-guide/).
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.
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 own `bianca` project.
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` :
In this guide, we use `rackham` to download and transfer files to the `wharf` area, but it can also be done on your own computer.
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.
`export NXF_SINGULARITY_CACHEDIR=Your_Location_For_The_Singularity_directory/.`
### Download and install Nextflow
You should now be able to run your nf-core pipeline on bianca.
You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# See the available versions for the module
module spider Nextflow
# Load a specific version of the Nextflow module
module load bioinfo-tools Nextflow/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Download the nextflow-all bundle
$ wget https://github.com/nextflow-io/nextflow/releases/download/v<NEXTFLOW_VERSION>/nextflow-<NEXTFLOW_VERSION>-all
# Connect to the wharf area using sftp
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
# Transfer nextflow to the wharf area
sftp> put nextflow-<NEXTFLOW_VERSION>-all .
# Exit sftp
$ exit
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your project
$ cd /castor/project/proj_nobackup
# Make folder for Nextflow
$ mkdir tools
$ mkdir tools/nextflow
# Move Nextflow from the wharf area to its directory
$ mv /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow
# Establish permission
$ chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
# If you want other people to use it
# Be sure that your group has rights to the directory as well
$ chown -R .<BIANCA_PROJECT> /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all
# Make a link to it
$ ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-<NEXTFLOW_VERSION>-all /castor/project/proj_nobackup/tools/nextflow/nextflow
# And every time you're launching Nextflow, don't forget to export the following ENV variables
# Or add them to your .bashrc file
$ export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
$ export PATH=${NXF_HOME}:${PATH}
$ export NXF_TEMP=$SNIC_TMP
$ export NXF_LAUNCHER=$SNIC_TMP
$ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-images
```
### Install nf-core tools
You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# See the available versions for the module
module spider nf-core
# Load a specific version of the nf-core module
module load bioinfo-tools nf-core/<VERSION>`
```
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Install the latest pip version
$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev --user
```
### Download and transfer a nf-core pipeline
```bash
# Connect to rackham
$ ssh -X <USER>@rackham.uppmax.uu.se
# Or stay in your terminal
# Open an interactive session (if you are on rackham)
$ interactive <rackham_project>
# Download a pipeline with the singularity images
$ nf-core download <PIPELINE> -r <PIPELINE_VERSION> -s --compress none
# If necessary, extra singularity images can be download separately
# For example, if you downloaded nf-core/sarek, you will need extra images for annotation
# Here we download the nf-core/sarek GRCh38 specific images
$ singularity pull --name nfcore-sareksnpeff-2.7.GRCh38.img docker://nfcore/sareksnpeff:2.7.GRCh38
$ singularity pull --name nfcore-sarekvep-2.7.GRCh38.img docker://nfcore/sarekvep:2.7.GRCh38
# Which can then be moved into the nf-core/sarek download folder
$ mv *.img nf-core-sarek-2.7/singularity-images/.
# Connect to the wharf area using sftp
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
# Transfer <PIPELINE> folder from rackham to the wharf area
sftp> put -r nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# The archives will be in the wharf folder in your user home on your bianca project
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your project
$ cd /castor/project/proj_nobackup
# Make and go into a nf-core directory (where you will store all nf-core pipelines')
$ mkdir nf-core
$ cd nf-core
# Move the folder from the wharf area to the project
$ cp /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# If you want other people to use it,
# Be sure that your group has rights to the directory as well
$ chown -R .<BIANCA_PROJECT> nf-core-<PIPELINE>-<PIPELINE_VERSION>
# Make a symbolic link to the extracted repository
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
```
The principle is to have every member of your project to be able to use the same `nf-core/<PIPELINE>` version at the same time.
So every member of the project who wants to use `nf-core/<PIPELINE>` will need to do:
```bash
# Connect to bianca
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your user directory
$ cd /home/<USER>
# Make a symbolic link to the default nf-core/<PIPELINE>
$ ln -s /castor/project/proj_nobackup/nf-core/nf-core-<PIPELINE>-default nf-core-<PIPELINE>
```
And then `nf-core/<PIPELINE>` can be used with:
```bash
# run <PIPELINE> on bianca
$ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
```
## Update a pipeline
To update, repeat the same steps as for installing and update the link.
```bash
# Connect to bianca (Connect to rackham first if needed)
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to the nf-core directory in your project
$ cd /castor/project/proj_nobackup/nf-core
# Remove link
$ unlink nf-core-<PIPELINE>-default
# Link to new nf-core/<PIPELINE> version
$ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
```
You can for example keep a `nf-core-<PIPELINE>-default` version that you are sure is working, an make a link for a `nf-core-<PIPELINE>-testing` or `nf-core-<PIPELINE>-development`.