First stub

UPPMAX · May 30, 2024 · 8442821 · 8442821
1 parent cfc52f9
commit 8442821
Show file tree

Hide file tree

Showing 22 changed files with 886 additions and 101 deletions.
diff --git a/README.md b/README.md
@@ -15,6 +15,13 @@ yet with ...
 
 This has been discussed with the main contributor to <https://github.com/UPPMAX/uppmax_intro>.
 
+## Credits
+
+Credits go to:
+
+- [The 'UPPMAX/uppmax_intro' contributors](https://github.com/UPPMAX/uppmax_intro/graphs/contributors)
+- [The 'UPPMAX/UPPMAX-documentation' contributors](https://github.com/UPPMAX/UPPMAX-documentation/graphs/contributors)
+
 ## Files used by continuous integration scripts
 
 Filename                              |Descriptions

diff --git a/docs/assets/UU_logo_color.svg b/docs/assets/UU_logo_color.svg
diff --git a/docs/assets/logo.svg b/docs/assets/logo.svg
diff --git a/docs/assets/logo_color.png b/docs/assets/logo_color.png
diff --git a/docs/backup.md b/docs/backup.md
@@ -0,0 +1 @@
+# Backup
diff --git a/docs/img/Bianca-transfer.png b/docs/img/Bianca-transfer.png
diff --git a/docs/img/c_557912-l_1-k_cram_compression.png b/docs/img/c_557912-l_1-k_cram_compression.png
diff --git a/docs/img/dds-cli.png b/docs/img/dds-cli.png
diff --git a/docs/img/filezilla-snapshot.png b/docs/img/filezilla-snapshot.png
diff --git a/docs/img/winscp-snaphot.png b/docs/img/winscp-snaphot.png
diff --git a/docs/img/winscp-snaphot1.png b/docs/img/winscp-snaphot1.png
diff --git a/docs/index.md b/docs/index.md
@@ -0,0 +1,31 @@
+---
+template: home.html
+---
+
+<center>
+
+<br/><br/>
+
+<img src="assets/UU_logo_color.svg" alt="drawing" width="200"/>
+
+<br/>
+
+
+# Welcome to the UPPMAX documentation
+
+
+<br/>
+
+[Apply for a project](getting_started/project_apply.md){ .md-button .md-button--primary }
+
+[:material-rocket-launch: Getting started](getting_started/get_started.md){: .md-button .md-button--primary }
+[:material-rocket-launch: Software](software/overview.md){: .md-button .md-button--primary }
+[:material-rocket-launch: Lost credentials for UPPMAX account](https://suprintegration.uppmax.uu.se/getpasswd){: .md-button .md-button--primary }
+[:material-alert-box: Migration to Dardel](cluster_guides/dardel_migration.md){ .md-button .md-button--primary }
+
+[:material-rocket-launch: Back to UPPMAX home](https://www.uu.se/en/centre/uppmax){: .md-button .md-button--primary }
+
+<br/><br/>
+
+
+</center>
diff --git a/docs/misc/misc_1.md b/docs/misc/misc_1.md
@@ -0,0 +1,3 @@
+# Session 1
+
+First session.
diff --git a/docs/sessions/session_1.md b/docs/sessions/session_1.md
@@ -0,0 +1,3 @@
+# Session 1
+
+First session.
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css
@@ -0,0 +1,65 @@
+/* Color Settings */
+/* https://github.com/squidfunk/mkdocs-material/blob/6b5035f5580f97532d664e3d1babf5f320e88ee9/src/assets/stylesheets/main/_colors.scss */
+/* https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#custom-colors */
+:root > * {
+  --md-primary-fg-color: #E6E6E6;
+  --md-primary-bg-color: #1d1d20;
+
+  --md-default-fg-color: #1d1d20;
+  --md-default-bg-color: #ffffff;
+
+  --md-code-fg-color: #1d1d20;
+
+  --md-accent-fg-color: #999;
+
+  --md-admonition-fg-color: #1d1d20;
+
+  --md-typeset-color: #1d1d20;
+  --md-typeset-a-color: #0645AD;
+
+  --md-footer-bg-color: #E6E6E6;
+  --md-footer-fg-color: #000000;
+
+}
+
+
+/* https://github.com/squidfunk/mkdocs-material/issues/4832#issuecomment-1374891676 */
+.md-nav__link[for] {
+  color: var(--md-default-fg-color) !important;
+}
+
+/* Center Markdown Tables (requires md_in_html extension) */
+.center-table {
+  text-align: center;
+}
+
+/* Reset alignment for table cells */
+.md-typeset .center-table :is(td, th):not([align]) {
+  text-align: initial;
+}
+
+  .md-typeset a {
+  text-decoration: underline;
+}
+
+
+/* Markdown Header */
+/* https://github.com/squidfunk/mkdocs-material/blob/dcab57dd1cced4b77875c1aa1b53467c62709d31/src/assets/stylesheets/main/_typeset.scss */
+.md-typeset h1 {
+  font-weight: 400;
+  color: var(--md-default-fg-color);
+}
+
+.md-typeset h2 {
+  font-weight: 400;
+}
+
+.md-typeset h3 {
+  font-weight: 500;
+}
+
+/* Image align center */
+.center {
+  display: block;
+  margin: 0 auto;
+}
diff --git a/docs/support.md b/docs/support.md
@@ -0,0 +1,11 @@
+# UPPMAX support
+
+- Want to help improve our documentation? Do a Pull Request to [the UPPMAX documentation GitHub repository](https://github.com/UPPMAX/UPPMAX-documentation)
+
+- Lost your password? You can [request a new password to your UPPMAX account here](https://suprintegration.uppmax.uu.se/getpasswd).
+
+- Please contact UPPMAX support through the [Support Form](https://supr.naiss.se/support/).
+    - or by emailing `support@uppmax.uu.se`. We are available during normal office hours.
+
+- For Uppsala University Education, support is provided through the UU IT Servicedesk.
+  [What should I think about when planning a course using UPPMAX resources](https://www.uu.se/en/centre/uppmax/get-started/create-account-and-apply-for-project/apply-for-projects/course/planning-a-course)
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,111 +1,17 @@
-site_name: UPPMAX Documentation
+site_name: UPPMAX Intro Day 1
 
-repo_url: https://github.com/UPPMAX/UPPMAX-documentation
+repo_url: https://github.com/UPPMAX/uppmax_intro_day_1
 
 nav:
   - Home: index.md
-  - Getting Started:
-    - Get started: getting_started/get_started.md
-    - Applying for a Project: getting_started/project_apply.md
-    - Accessing UPPMAX:
-      - Get inside the university networks: getting_started/get_inside_sunet.md
-      - Log in to Bianca: getting_started/login_bianca.md
-      - Log in to Dardel: getting_started/login_dardel.md
-      - Log in to Rackham: getting_started/login_rackham.md
-      - Log in to Snowy: getting_started/login_snowy.md
-    - Linux tutorials:
-      - Working in Linux: getting_started/linux.md
-      - Basic Linux commands: getting_started/linux_basics.md
-#    - Running your first job: getting_started/first_job.md
-  - Cluster user guide:
-    - The UPPMAX clusters: cluster_guides/uppmax_cluster.md
-    - Clusters: 
-      - Bianca: cluster_guides/bianca.md
-      - Dardel: cluster_guides/dardel.md
-      - Rackham: cluster_guides/rackham.md
-      - Snowy: cluster_guides/snowy.md
-    - General cluster tools: 
-      - Start an interactive node: cluster_guides/start_interactive_node.md
-      - Modules: cluster_guides/modules.md
-      - Slurm: cluster_guides/slurm.md
-      - Managing your project: cluster_guides/project_management.md
-    - Running jobs:
-      - Checking and optimizing jobs: cluster_guides/optimizing_jobs.md
-      - Runtime tips: cluster_guides/running_jobs/runtime_tips.md
-      - Storage and compression: cluster_guides/running_jobs/storage_compression.md
-      - Screen: cluster_guides/screen.md
-    - Data transfer: 
-      - Transfer to/from Bianca: cluster_guides/transfer_bianca.md
-      - Migrate to Dardel: cluster_guides/dardel_migration.md
-      - Transfer to/from Rackham: cluster_guides/transfer_rackham.md
-    - Installing and development: 
-      - Installing: cluster_guides/install.md
-      - Installing with conda: cluster_guides/conda.md
-      - Compilers: software/compilers.md
-      - Compiling serial code: cluster_guides/compiling_serial.md
-      - Compiling parallel code: cluster_guides/compiling_parallel.md
-      - Debuggers: software/debuggers.md
-      - Profilers: software/profilers.md
-      - Singularity/Apptainer: cluster_guides/singularity.md
-      - Spack: software/spack.md
-  - Software:
-    - Overview: software/overview.md
-    - Software table: software/software-table.md
-    - Text editors: software/text_editors.md
-    - Software-specific documentation:      
-      - Chemistry/physics/atmosphere:
-        - GAMESS_US: software/games_us.md
-        - Gaussian: software/gaussian.md
-        - GROMACS: software/gromacs.md
-        - Molcas: software/openmolcas.md
-        - WRF: software/wrf.md
-      - Integrated development environments (IDE):
-        - Jupyter: software/jupyter.md
-        - RStudio: software/rstudio.md
-        - VSCode: software/vscode.md
-        - VSCodium: software/vscodium.md
-      - Life Science: 
-        - BEAST: software/beast.md
-        - BEAST2: software/beast2.md
-        - Cram: software/cram.md
-        - IGV: software/igv.md
-        - MetONTIIME: software/metontiime.md
-        - Tracer: software/tracer.md
-      - Machine Learning and AI:
-        - NVIDIA DLF: software/nvidia-deep-learning-frameworks.md
-        - TensorFlow: software/tensorflow.md
-        - Whisper: software/whisper.md
-      - Programming languages:
-        - Julia: software/julia.md
-        - MATLAB: software/matlab.md
-        - Python: software/python.md
-        - Perl: software/perl.md
-        - R: software/r.md
-      - Misc tools:
-        - darsync: cluster_guides/darsync.md
-        - jobstats: software/jobstats.md
-        - projplot: software/projplot.md
-        - Rclone: software/rclone.md      
-        - SSH: software/ssh.md
-        - SFTP: software/sftp.md
-        - ThinLinc: software/thinlinc.md
-
-  - Databases: 
-     - Overview: databases/overview.md
-     - BLAST databases available locally: databases/blast.md
-     - NCBI taxonomy databases: databases/ncbi.md
-     - DIAMOND protein alignment databases: databases/diamond.md
-     - Reference genomes: databases/reference_genomes.md
-     - 1000-genome project: databases/1000-genome_project.md
-     - Simons Genome Diversity Project datasets: databases/simons_genome.md
-     - Other bioinformatics-oriented local data resources: databases/other_local.md
-
-#  - Workshops and courses: workshops_courses/workshops_courses.md
-  - Support: support.md
+  - Sessions:
+    - Session 1: sessions/session_1.md
+  - Misc:
+    - Misc 1: misc/misc_1.md
 
 theme:
   name: material
-  greetings: Welcome to UPPMAX userguide
+  greetings: Welcome to UPPMAX Intro Day 1
   font:
     text: Lato
     code: JetBrains Mono

diff --git a/mkdocs_uppmax/home.html b/mkdocs_uppmax/home.html
@@ -0,0 +1,65 @@
+{% extends "main.html" %}
+
+
+{% block tabs %}
+  {{ super() }}
+
+
+  <style>
+
+    /* Application header should be static for the landing page */
+    <!-- .md-header { -->
+    <!--   position: initial; -->
+    <!-- } -->
+
+    /* Remove spacing, as we cannot hide it completely */
+    .md-main__inner {
+      margin: 0;
+    }
+
+    /* Hide main content for now */
+    <!-- .md-content { -->
+    <!--   display: none; -->
+    <!-- } -->
+
+    /* Hide table of contents */
+    @media screen and (min-width: 60em) {
+      .md-sidebar--secondary {
+        display: none;
+      }
+    }
+
+    /* Hide navigation */
+    @media screen and (min-width: 76.25em) {
+      .md-sidebar--primary {
+        display: none;
+      }
+    }
+
+  </style>
+
+  <section class="tx-container">
+
+    <div class="md-grid md-typeset">
+
+      {{ page.content }}
+
+{% endblock %}
+
+
+{% block content %}{% endblock %}
+
+{% block footer %}
+<!--<footer class="md-footer">
+   <div class="md-footer-meta md-typeset">
+     <div class="md-footer-meta__inner md-grid"> 
+       <div > 
+         <h2>Contact UPPMAX</h2> 
+       </div>
+     </div>
+   </div>
+
+</footer>
+-->
+{% endblock %}
+
diff --git a/mkdocs_uppmax/partials/footer.html b/mkdocs_uppmax/partials/footer.html
@@ -0,0 +1,39 @@
+<!-- <footer class="md-footer"> -->
+<!--   <div class="md-footer-meta md-typeset"> -->
+<!--     <div class="md-footer-meta__inner md-grid"> -->
+<!--       <div > -->
+<!--         <h2>Contact UPPMAX</h2> -->
+<!--         <div> -->
+<!--           <ul> -->
+<!--             <li>Support: <a href="mailto:support@uppmax.uu.se">support@uppmax.uu.se</a></li> -->
+<!--             <li>Director: <a href="http://katalog.uu.se/profile/?id=N94-2143">Elisabeth Larsson</a></li> -->
+<!--             <li>Economy: <a href="http://katalog.uu.se/empinfo/?id=N18-298">Wiola &Ouml;hlund</a></li> -->
+<!--             <li>Post: P.O. Box 337, 751 05 Uppsala</li> -->
+<!--           </ul> -->
+<!--         </div> -->
+<!--       </div> -->
+<!--       <div > -->
+<!--         <h2>Visit UPPMAX</h2> -->
+<!--         <div> -->
+<!--           <ul> -->
+<!--             <li>Floor 3, House 10, &Aring;ngstr&ouml;m Laboratory</li> -->
+<!--             <li>L&auml;gerhyddsv&auml;gen 1</li> -->
+<!--             <li>752 37 Uppsala</li> -->
+<!--           </ul> -->
+<!--         </div> -->
+<!--       </div> -->
+<!--       <div> -->
+<!--         <h2>Shortcuts</h2> -->
+<!--         <div> -->
+<!--           <p style="text-align:start"><a href="/support/getting-started/">Apply for a project&nbsp;or user account</a> -->
+<!--           </p> -->
+<!--           <p style="text-align:start"><a href="/support/faq/">FAQ</a></p> -->
+<!--           <p style="text-align:start"><a href="/support/user-guides/">User Guides</a></p> -->
+<!--           <p style="text-align:start"><a href="/resources/software/installed-software/">List of Installed Software</a> -->
+<!--           </p> -->
+<!--         </div> -->
+<!--       </div> -->
+<!--     </div> -->
+<!--   </div> -->
+<!---->
+<!-- </footer> -->
diff --git a/mkdocs_uppmax/stylesheets/extra.css b/mkdocs_uppmax/stylesheets/extra.css
@@ -0,0 +1,5 @@
+:root > * {
+  --md-primary-fg-color:        #EE0F0F;
+  --md-primary-fg-color--light: #ECB7B7;
+  --md-primary-fg-color--dark:  #90030C;
+}
diff --git a/scripts/check_links.sh b/scripts/check_links.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+#
+# Check links
+#
+# Usage:
+#
+#   ./scripts/check_links.sh
+
+if [[ "$PWD" =~ scripts$ ]]; then
+    echo "FATAL ERROR."
+    echo "Please run the script from the project root. "
+    echo "Present working director: $PWD"
+    echo " "
+    echo "Tip: like this"
+    echo " "
+    echo "  ./scripts/check_links.sh"
+    echo " "
+    exit 42
+fi
+
+markdown-link-check --config mlc_config.json --quiet docs/**/*.md