diff --git a/docs/uppmax.md b/docs/uppmax.md index 9057b2a..a38c1be 100644 --- a/docs/uppmax.md +++ b/docs/uppmax.md @@ -168,8 +168,8 @@ $ ssh -X @rackham.uppmax.uu.se # Open an interactive session (if you are on rackham) $ interactive -# Download a pipeline (nf-core/rnaseq 3.0) with the singularity images -$ nf-core download rnaseq -r 3.0 -s --compress none +# Download a pipeline with the singularity images +$ nf-core download -r -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 @@ -183,8 +183,8 @@ $ mv *.img nf-core-sarek-2.7/singularity-images/. # Connect to the wharf area using sftp $ sftp -@bianca-sftp.uppmax.uu.se:- -# Transfer rnaseq folder from rackham to the wharf area -sftp> put -r nf-core-rnaseq-3.0 . +# Transfer folder from rackham to the wharf area +sftp> put -r nf-core-- . # 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 # Move the folder from the wharf area to the project -$ cp /castor/project/proj_nobackup/wharf//-/nf-core-rnaseq-3.0 . +$ cp /castor/project/proj_nobackup/wharf//-/nf-core-- . # If you want other people to use it, # Be sure that your group has rights to the directory as well -$ chown -R . nf-core-rnaseq-3.0 +$ chown -R . nf-core-- # Make a symbolic link to the extracted repository -$ ln -s nf-core-rnaseq-3.0 nf-core-rnaseq-default +$ ln -s nf-core-- nf-core--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. -So every member of the project who wants to use nf-core/rnaseq will need to do: +The principle is to have every member of your project to be able to use the same nf-core/ version at the same time. +So every member of the project who wants to use nf-core/ will need to do: ```bash # Connect to bianca @@ -219,15 +219,15 @@ $ ssh -A -@bianca.uppmax.uu.se # Go to your user directory $ cd /home/ -# Make a symbolic link to the default nf-core/rnaseq -$ ln -s /castor/project/proj_nobackup/nf-core/nf-core-rnaseq-default nf-core-rnaseq +# Make a symbolic link to the default nf-core/ +$ ln -s /castor/project/proj_nobackup/nf-core/nf-core--default nf-core- ``` -And then nf-core/rnaseq can be used with: +And then nf-core/ can be used with: ```bash -# run rnaseq on bianca -$ nextflow run ~/rnaseq -profile uppmax --project --genome [GENOME ASSEMBLY] ... +# run on bianca +$ nextflow run ~/ -profile uppmax --project --genome ... ``` ## 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) $ ssh -A -@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 # Remove link -$ unlink nf-core-rnaseq-default +$ unlink nf-core--default -# Link to new nf-core/rnaseq version -$ ln -s nf-core-rnaseq-3.0 nf-core-rnaseq-default +# Link to new nf-core/ version +$ ln -s nf-core-- nf-core--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--default` version that you are sure is working, an make a link for a `nf-core--testing` or `nf-core--development`.