Merge branch 'dev' into Manifest

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 -   [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule
 -   [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Update Nextflow to `0.32.0`
+-   [#660](https://github.com/SciLifeLab/Sarek/pull/660) - Update docs
 
 ### `Fixed`
 

docs/INSTALL_BIANCA.md

@@ -12,21 +12,13 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 > ssh -AX [USER]@rackham.uppmax.uu.se
 # Or just open a terminal
 
-# create directories
-> mkdir nextflow_install
-> cd nextflow_install
+# Download the all Nextflow bundle
+> wget https://github.com/nextflow-io/nextflow/releases/download/v[xx.yy.zz]/nextflow-[xx.yy.zz]-all
 
-# Install Nextflow
-> curl -s https://get.nextflow.io | bash
-> cd ..
-
-# Archive Nextflow
-> tar czvf nextflow_v[xx.yy.zz].tgz .nextflow nextflow_install/nextflow
-
-# Send the tar to bianca (here using sftp)
+# Send to bianca (here using sftp)
 # For FileZilla follow the bianca user guide
 > sftp [USER]-[PROJECT]@bianca-sftp.uppmax.uu.se:[USER]-[PROJECT]
-> put nextflow_v[xx.yy.zz].tgz
+> put nextflow-[xx.yy.zz]-all
 
 # Exit sftp
 > exit
@@ -37,37 +29,28 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 # Go to your project
 > cd /castor/project/proj_nobackup
 
-# Make and go into a Nextflow directoy
+# Make directory for Nextflow
 > mkdir tools
 > mkdir tools/nextflow
-> cd tools/nextflow
-
-# Copy the tar from wharf to the project
-> cp /castor/project/proj_nobackup/wharf/[USER]/[USER]-[PROJECT]/nextflow_v[xx.yy.zz].tgz /castor/project/proj_nobackup/tools/nextflow
-
-# extract Nextflow
-> tar xzvf nextflow_v[xx.yy.zz].tgz
 
-# Move files
-> mv .nextflow nextflow_v[xx.yy.zz]
-> mv nextflow_install nextflow_v[xx.yy.zz]/bin
+# Move Nextflow from wharf to its directory
+> mv /castor/project/proj_nobackup/wharf/[USER]/[USER]-[PROJECT]/nextflow-[xx.yy.zz]-all /castor/project/proj_nobackup/tools/nextflow
 
-# Establish permission for some files
-> chmod 755 nextflow_v[xx.yy.zz]/bin/nextflow
-> chmod 660 nextflow_v[xx.yy.zz]/framework/[xx.yy.zz]/nextflow-[xx.yy.zz]-one.jar
+# Establish permission
+> chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all
 
 # If you want other people to use it
 # Be sure that your group has rights to the directory as well
 
-> chown -R .[PROJECT] nextflow_v[xx.yy.zz]
+> chown -R .[PROJECT] /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all
 
-# Clean directory
-> rm nextflow_v[xx.yy.zz].tgz
+# Make a link to it
+> ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all /castor/project/proj_nobackup/tools/nextflow/nextflow
 
 # And everytime 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/nextflow_v[xx.yy.zz]
-> export PATH=${NXF_HOME}/bin:${PATH}
+> export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
+> export PATH=${NXF_HOME}:${PATH}
 > export NXF_TEMP=$SNIC_TMP
 > export NXF_LAUNCHER=$SNIC_TMP
 ```