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feat: use <PIPLEINE>

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MaxUlysse 2021-04-21 11:17:06 +02:00
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docs/uppmax.md
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@ -168,8 +168,8 @@ $ ssh -X <USER>@rackham.uppmax.uu.se
# Open an interactive session (if you are on rackham) # Open an interactive session (if you are on rackham)
$ interactive <rackham_project> $ interactive <rackham_project>
# Download a pipeline (nf-core/rnaseq 3.0) with the singularity images # Download a pipeline with the singularity images
$ nf-core download rnaseq -r 3.0 -s --compress none $ nf-core download <PIPELINE> -r <PIPELINE_VERSION> -s --compress none
# If necessary, extra singularity images can be download separately # If necessary, extra singularity images can be download separately
# For example, if you downloaded nf-core/sarek, you will need extra images for annotation # For example, if you downloaded nf-core/sarek, you will need extra images for annotation
@ -183,8 +183,8 @@ $ mv *.img nf-core-sarek-2.7/singularity-images/.
# Connect to the wharf area using sftp # Connect to the wharf area using sftp
$ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT> $ sftp <USER>-<BIANCA_PROJECT>@bianca-sftp.uppmax.uu.se:<USER>-<BIANCA_PROJECT>
# Transfer rnaseq folder from rackham to the wharf area # Transfer <PIPELINE> folder from rackham to the wharf area
sftp> put -r nf-core-rnaseq-3.0 . sftp> put -r nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# The archives will be in the wharf folder in your user home on your bianca project # The archives will be in the wharf folder in your user home on your bianca project
@ -199,18 +199,18 @@ $ mkdir nf-core
$ cd nf-core $ cd nf-core
# Move the folder from the wharf area to the project # Move the folder from the wharf area to the project
$ cp /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nf-core-rnaseq-3.0 . $ cp /castor/project/proj_nobackup/wharf/<USER>/<USER>-<BIANCA_PROJECT>/nf-core-<PIPELINE>-<PIPELINE_VERSION> .
# If you want other people to use it, # If you want other people to use it,
# Be sure that your group has rights to the directory as well # Be sure that your group has rights to the directory as well
$ chown -R .<BIANCA_PROJECT> nf-core-rnaseq-3.0 $ chown -R .<BIANCA_PROJECT> nf-core-<PIPELINE>-<PIPELINE_VERSION>
# Make a symbolic link to the extracted repository # Make a symbolic link to the extracted repository
$ ln -s nf-core-rnaseq-3.0 nf-core-rnaseq-default $ 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/rnaseq version at the same time. 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/rnaseq will need to do: So every member of the project who wants to use nf-core/<PIPELINE> will need to do:
```bash ```bash
# Connect to bianca # Connect to bianca
@ -219,15 +219,15 @@ $ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to your user directory # Go to your user directory
$ cd /home/<USER> $ cd /home/<USER>
# Make a symbolic link to the default nf-core/rnaseq # Make a symbolic link to the default nf-core/<PIPELINE>
$ ln -s /castor/project/proj_nobackup/nf-core/nf-core-rnaseq-default nf-core-rnaseq $ ln -s /castor/project/proj_nobackup/nf-core/nf-core-<PIPELINE>-default nf-core-<PIPELINE>
``` ```
And then nf-core/rnaseq can be used with: And then nf-core/<PIPELINE> can be used with:
```bash ```bash
# run rnaseq on bianca # run <PIPELINE> on bianca
$ nextflow run ~/rnaseq -profile uppmax --project <BIANCA_PROJECT> --genome [GENOME ASSEMBLY] ... $ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
``` ```
## Update a pipeline ## Update a pipeline
@ -238,14 +238,14 @@ To update, repeat the same steps as for installing and update the link.
# Connect to bianca (Connect to rackham first if needed) # Connect to bianca (Connect to rackham first if needed)
$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se $ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
# Go to the rnaseq directory in your project # Go to the nf-core directory in your project
$ cd /castor/project/proj_nobackup/nf-core $ cd /castor/project/proj_nobackup/nf-core
# Remove link # Remove link
$ unlink nf-core-rnaseq-default $ unlink nf-core-<PIPELINE>-default
# Link to new nf-core/rnaseq version # Link to new nf-core/<PIPELINE> version
$ ln -s nf-core-rnaseq-3.0 nf-core-rnaseq-default $ ln -s nf-core-<PIPELINE>-<PIPELINE_VERSION> nf-core-<PIPELINE>-default
``` ```
You can for example keep a `nf-core-rnaseq-default` version that you are sure is working, an make a link for a `nf-core-rnaseq-testing` or `nf-core-rnaseq-development`. 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`.