diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ad0f17ef2..e226106c9e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Changed` - [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule +- [#660](https://github.com/SciLifeLab/Sarek/pull/660) - Update docs ### `Fixed` diff --git a/docs/INSTALL_BIANCA.md b/docs/INSTALL_BIANCA.md index 5f10e7247e..2137a24032 100644 --- a/docs/INSTALL_BIANCA.md +++ b/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 ```