Update Docs

CHANGELOG.md

@@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#678](https://github.com/SciLifeLab/Sarek/pull/678) - Changing VEP to v92 and adjusting CPUs for VEP
 -   [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script
 -   [#671](https://github.com/SciLifeLab/Sarek/pull/671) - publishDir modes are now params
--   [#677](https://github.com/SciLifeLab/Sarek/pull/677), [#698](https://github.com/SciLifeLab/Sarek/pull/698) - Update docs
+-   [#677](https://github.com/SciLifeLab/Sarek/pull/677), [#698](https://github.com/SciLifeLab/Sarek/pull/698), [#703](https://github.com/SciLifeLab/Sarek/pull/703) - Update docs
 -   [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Update old awsbatch configuration
 -   [#682](https://github.com/SciLifeLab/Sarek/pull/682) - Specifications for memory and cpus for awsbatch
 -   [#693](https://github.com/SciLifeLab/Sarek/pull/693) - Qualimap bamQC is now ran after mapping and after recalibration for better QC

conf/uppmax-localhost.config

@@ -12,6 +12,7 @@ env {
 }
 
 params {
+  containerPath = '/sw/data/uppnex/ToolBox/sarek'
   genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
   singleCPUMem  = 8.GB
   totalMemory = 104.GB // change to 240 on irma

conf/uppmax-slurm.config

@@ -7,6 +7,7 @@
  */
 
 params {
+  containerPath = '/sw/data/uppnex/ToolBox/sarek'
   genome_base = params.genome == 'GRCh37' ? '/sw/data/uppnex/ToolBox/ReferenceAssemblies/hg38make/bundle/2.8/b37' : params.genome == 'GRCh38' ? '/sw/data/uppnex/ToolBox/hg38bundle' : 'References/smallGRCh37'
   runTime       = 48.h
   singleCPUMem  = 7.GB // for processes that are using more memory but a single CPU only. Use the 'core' queue for these

docs/INSTALL_BIANCA.md

@@ -58,10 +58,11 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 ## Install Sarek
 
 Sarek use Singularity containers to package all the different tools.
+All containers are already stored on UPPMAX.
 
-As `bianca` is secure, no direct download is available, so Sarek and the Singularity containers will have to be installed and updated manually.
+As `bianca` is secure, no direct download is available, so Sarek will have to be installed and updated manually.
 
-You can either download Sarek and the containers on your computer (you will need Nextflow and Singularity for that) or on `rackham`, make an archive, and send it to `bianca` using `FileZilla` or `sftp` given your preferences.
+You can either download Sarek on your computer or on `rackham`, make an archive, and send it to `bianca` using `FileZilla` or `sftp` given your preferences.
 
 All Reference files are already stored in `bianca`.
 
@@ -108,18 +109,6 @@ Wrote Sarek-[snapID].tar.gz
 > put Sarek-[snapID].tar.gz
 > exit
 
-# To get the containers
-# This script will need Singularity and Nextflow installed
-# If executed on Rackham: The script needs to be started from an interactive session
-# with at least two cores and approximately 3 hours. The scripts will write about
-# 12 Gb data to ~/.singularity, so this amount of disk space needs to be available
-# in the users home directory on Rackham.
-#
-> ./scripts/do_all.sh --pull --tag <VERSION>
-
-# Send the containers to bianca using the same method
-# They will be in the containers/ directory as .img files
-
 # The archive will be in the wharf folder in your user home on your bianca project
 
 # Connect to bianca

docs/INSTALL_RACKHAM.md

@@ -13,10 +13,7 @@ The Reference files are already stored in `rackham`.
 Nextflow will automatically fetch Sarek from GitHub when launched if `SciLifeLab/Sarek` is specified as the workflow name.
 
 Sarek use Singularity containers to package all the different tools.
-
-On `rackham` you do have the possibility to use the automatic pull of the containers.
-
-You can choose a specific location to store these, otherwise they will be stored in the directory where you're running Sarek.
+All containers are already stored on UPPMAX.
 
 ## Test Sarek with small dataset and small reference