fix: first draft of bianca guide

docs/uppmax.md

@@ -19,7 +19,7 @@ You can do this with the `--project` flag (two hyphens) when launching nextflow.
 nextflow run nf-core/PIPELINE -profile uppmax --project snic2018-1-234 # ..rest of pipeline flags
 ```
 
-> NB: If you're not sure what your UPPMAX project ID is, try running `groups` or checking SUPR.
+$ 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.
 
@@ -43,7 +43,7 @@ If your nf-core pipeline run is running out of memory, you can run on a fat node
 ```
 
 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.
 
@@ -76,12 +76,172 @@ To use it, submit with `-profile uppmax,devel`.
 
 ## 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 about `bianca`, follow the [UPPMAX `bianca` user guide](http://uppmax.uu.se/support/user-guides/bianca-user-guide/).
+$ :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).
+ > :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/).
 
-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 wharf, 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 Nextflow
 
-You should now be able to run your nf-core pipeline on bianca.
+You can use the 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
+# 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 wharf using sftp
+# For FileZilla follow the bianca user guide
+$ sftp <user>-<bianca_project>@bianca-sftp.uppmax.uu.se:<user>-<bianca_project>
+
+# Transfer nextflow to wharf
+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 wharf 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
+```
+
+### Download nf-core pipelines
+
+```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>
+
+# Install the latest pip version
+$ pip3 install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev --user
+
+# Download a pipeline (nf-core/rnaseq 3.0) with the singularity images
+$ nf-core download rnaseq -r 3.0 -s -p 10 --compress none
+
+# Download a pipeline (nf-core/sarek 2.7) with the singularity images
+$ nf-core download sarek -r 2.7 -s -p 10 --compress none
+
+# Download specific Singularity 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
+
+# Move specific Singularity images into nf-core download folder
+$ mv *.img nf-core-sarek-2.7/singularity-images/.
+
+# Connect to wharf using sftp
+$ sftp <user>-<bianca_project>@bianca-sftp.uppmax.uu.se:<user>-<bianca_project>
+
+# Transfer rnaseq folder from rackham to wharf
+sftp> put -r nf-core-rnaseq-3.0 .
+[...]
+
+# Transfer sarek folder from rackham to wharf
+sftp> put -r nf-core-sarek-2.7 .
+[...]
+
+# 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/sarek directory (where you will store all nf-core/sarek versions)
+$ mkdir sarek
+$ cd sarek
+
+# Copy the tar from wharf to the project
+$ cp /castor/project/proj_nobackup/wharf/<user>/<user>-<bianca_project>/nf-core-sarek-2.7 /castor/project/proj_nobackup/sarek
+
+# 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-sarek-2.7
+
+# Make a symbolic link to the extracted repository
+$ ln -s nf-core-sarek-2.7 default
+```
+
+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:
+
+```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/sarek
+$ ln -s /castor/project/proj_nobackup/sarek/default sarek
+```
+
+And then nf-core/sarek can be used with:
+
+```bash
+$ nextflow run ~/sarek -profile uppmax --project <bianca_project> --genome [GENOME ASSEMBLY] ...
+```
+
+This is an example of how to run sarek with the tool Manta and the genome assembly version GRCh38, which worked on `bianca` 20210416
+
+```bash
+$ nextflow run ~/sarek -profile uppmax --project <bianca_project> --tools Manta --input <input.tsv>
+```
+
+## Update nf-core/sarek
+
+Repeat the same steps as for installing nf-core/sarek, 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 sarek directory in your project
+$ cd /castor/project/proj_nobackup/sarek
+
+# Remove link
+$ rm default
+
+# Link to new nf-core/sarek version
+$ ln -s nf-core-sarek-2.7 default
+```
+
+You can for example keep a `default` version that you are sure is working, an make a link for a `testing` or `development`