Merge branch 'main' of https://github.com/UPPMAX/bianca_workshop

.github/workflows/check_links.yaml

@@ -0,0 +1,26 @@
+name: Check links
+
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 2 * *"
+
+
+jobs:
+  check_links:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: gaurav-nelson/github-action-markdown-link-check@v1
+
+      # Cannot deal with emails :-/
+      #- uses: lycheeverse/[email protected]
+      #  with:
+      #    #args: --verbose --exclude-mail './**/*.md' './**/*.html'
+      #    fail: true

.github/workflows/check_spelling.yaml

@@ -0,0 +1,27 @@
+# Check that there is correct spelling in all files
+name: Check spelling
+
+on:
+  push:
+  pull_request:
+  schedule:
+  - cron: "0 0 16 * *"
+
+
+jobs:
+  check_spelling:
+
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+
+      - name: Set up Git repository
+        uses: actions/checkout@v2
+
+      - name: Remove folders that do not care about spelling
+        run: |
+          rm -rf DevelopmentDesign
+          rm -rf feedback
+
+      - uses: igsekor/[email protected]

.spellcheck.yml

@@ -0,0 +1,24 @@
+matrix:
+- name: markdown
+  dictionary:
+    wordlists:
+    - .wordlist.txt
+    output: wordlist.dic
+    encoding: utf-8
+  pipeline:
+  - pyspelling.filters.markdown:
+      markdown_extensions:
+      - markdown.extensions.extra:
+  - pyspelling.filters.html:
+      comments: false
+      attributes:
+      - alt
+      ignores:
+      - ':matches(code, pre)'
+      - 'code'
+      - 'pre'
+      - 'blockquote'
+  sources:
+  - '**/*.md'
+  default_encoding: utf-8
+

.wordlist.txt

@@ -0,0 +1,204 @@
+Ångström
+Bilderbeek
+Björn
+BMC
+Claremar
+Dahlö
+Eklund
+Iusan
+Lindberg
+Lundberg
+Mitev
+Mitev's
+NBIS
+Pavlin
+Rackham
+Richel
+Richèl
+SCoRe
+Sjöman
+Söderberg
+UPPMAX
+
+analyse
+anonymisation
+Anonymised
+anonymised
+Apptainer
+apptainer
+authenticator
+automatical
+Automatical
+bam
+BAM
+bianca
+BioConductor
+bioinfo
+bioinformatics
+biometric
+CentOS
+chmod
+codeready
+Conda
+conda
+CONDA
+cp
+CRAN
+cran
+Crex
+devcore
+devel
+dir
+dirs
+dockerhub
+Dockerhub
+Domus
+DPIA
+eKQ
+ENVS
+EPEL
+fastq
+FileZilla
+Filezilla
+gatk
+GATK
+GDC
+gdc
+GDPR
+ggplot
+github
+gitlab
+GPUs
+grus
+hackmd
+HackMD
+harbour
+HPC
+html
+https
+Huawei
+ies
+IGV
+IMY
+io
+ipykernel
+IqCbOiyS
+julia
+Jupyter
+jupyter
+Keypoints
+keypoints
+LFTP
+libsolv
+LifeScience
+LMOD
+Lutra
+MacOS
+Miarka
+miniconda
+mkdocs
+Multithreading
+NAISS
+naiss
+nd
+NGI
+Nvidia
+ogv
+openmpi
+organisation
+Organisational
+personuppgifter
+pmitev
+powertools
+pre
+precompiled
+prerequsites
+proj
+projectB
+projid
+Pseudonymisation
+Pseudonymised
+PUBA
+rackham
+RaspBerry
+RaspberryPi
+Readthedocs
+Renviron
+reproducibility
+RfsmQQu
+RHEL
+Rpackage
+rpackages
+RStudio
+Rstudio
+rsync
+runtime
+sam
+sbatch
+scp
+SCP
+se
+sftp
+SFTP
+Skydd
+Slurm
+slurm
+SND
+SNIC
+snpEff
+SSD
+subfolder
+subfolders
+summarises
+summarising
+Sunet
+SUNET
+Supercomputing
+supercomputing
+SUPR
+Swegen
+sylabs
+syslabs
+SZ
+TCGA
+ThinLinc
+Thinlinc
+ThinLink
+Tidycmprsk
+tidycmprsk
+tranfer
+Transfering
+txt
+unallocated
+UpHg
+UppMACS
+uppmax
+Uppmax
+Uppsala
+Uqpa
+UU
+uu
+UU's
+VCF
+vCPU
+venv
+verysecret
+VerySecret
+VPN
+walltime
+wharfs
+WinSCP
+www
+Xeon
+XH
+xNVIDIA
+yaml
+Yhm
+zH
+alongs
+type-alongs
+repo
+SciLifeLab
+scilifelab
+dds-cli
+cli

docs/devel.md

@@ -36,7 +36,7 @@
     - and transfer back to Bianca via ``wharf``  
 - A little cumbersome but doable!
 
-- For collaboration within a ``sens`` project your can have a "local" ``remote`` repo in yor common project folder. 
+- For collaboration within a ``sens`` project your can have a "local" ``remote`` repo in your common project folder. 
 - [More on Git on Bianca](https://www.uppmax.uu.se/support/faq/software-faq/git-on-bianca/)
 
 

docs/index.md

@@ -21,11 +21,12 @@ template: home.html
     - If yes, welcome to a full day introduction to handling sensitive data on the UPPMAX cluster, Bianca. 
     - We will tell you about 
 
-        - NAISS-SENS, 
+        - NAISS-SENS: Legal and administrative aspects, 
         - how to login to Bianca, 
-        - transfer files via ``wharf``, 
-        - Slurm and the module system, 
-        - and how to work with Conda packages.
+        - some differences from Rackham
+        - transferring files via ``wharf``, 
+        - modules and job schedules system, 
+        - and how to do own installations.
 
 <center>
 <br>

docs/login_bianca.md

@@ -35,7 +35,7 @@
 ![Bianca](./img/biancaorganisation-01.png)
 
 - Bianca is only accessible from within Sunet (i.e. from university networks).
-- Use VPN outside Sunet. [Link to VPN for UU](https://mp.uu.se/en/web/info/stod/it-telefoni/it-support/network-on-campus/vpn-service)
+- Use VPN outside Sunet. [Link to VPN for UU](https://mp.uu.se/en/web/info/stod/it-telefoni/anvandarguider/network/vpn-service)
   - You can get VPN credentials from all Swedish universities.
 
 <br>

docs/naiss-sens-bianca.md

@@ -7,6 +7,7 @@
 
 This page summarises the content of [this presentation](https://github.com/UPPMAX/bianca_workshop/blob/main/docs/presentations/NAISS%20SENS%2C%20sensitive%20data%2C%20and%20Bianca.pdf).
 
+
 ## Sensitive personal data
 
 - Personal data: Traced to now living persons, e.g.
@@ -108,7 +109,8 @@ But how do you know whether data is anonymised?
 ![Image](./img/biancaorganisation-01.png)
 
 - Bianca is only accessible from within Sunet (i.e. from university networks).
-- Use VPN outside Sunet. [Link to VPN for UU](https://mp.uu.se/en/web/info/stod/it-telefoni/it-support/network-on-campus/vpn-service)
+- Use VPN outside Sunet. [Link to VPN for UU](https://mp.uu.se/en/web/info/stod/it-telefoni/anvandarguider/network/vpn-service)
+
     - You can get VPN credentials from all Swedish universities.
 
 <br>

docs/overview.md

@@ -15,7 +15,7 @@
 - From the users' perspective, there will initially only be minimal differences between the SNIC and NAISS regimes.
     - FAQ:s — <https://www.naiss.se/>
 - Application rounds: <https://www.naiss.se//#application-rounds-for-compute-and-storage-resources>
-- NAISS and Uppsala University fund UPPMAX — UU’s supercomputing center.
+- NAISS and Uppsala University fund UPPMAX — UU's supercomputing center.
 
 
 ## UPPMAX missions