Fix markdown style issues

docs/cluster_guides/install.md

@@ -3,12 +3,13 @@
 ## Install software yourself
 
 ### Build from source
+
 - To build from source use a **compiler module**
 - We have several compiler versions from GNU and INTEL
 - check with: ``$ ml avail gcc`` and ``$ ml avail intel``
 - [Guide for compiling **serial** programs](compiling_serial.md)
 - [Guide for compiling **parallel** programs](compiling_parallel.md)
-    - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
+  - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
 
 
 ## Packages and libraries to scripting programs
@@ -53,8 +54,8 @@
 
 - On UPPMAX the module ``R_packages`` is an omnibus package library containing almost all packages in the CRAN and BioConductor repositories.
 - As of 2023-05-31, there were a total of 23100 R packages installed in ``R_packages/4.2.1``.
-    -  A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1``
-    -  The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere.
+  - A total of 23109 packages were available in CRAN and BioConductor, and 23000 of these were installed in ``R_packages/4.2.1``
+  - The additional 100 R packages available in this module were installed from the CRAN/BioConductor archives, or were hosted on github, gitlab or elsewhere.
 
 - [Installing R packages](../software/r.md)
 
@@ -75,7 +76,7 @@
 
 - [Installing julia packages](http://docs.uppmax.uu.se/software/julia/#how-to-install-personal-packages)
 
-## "Containers"
+## Containers
 
 !!! info
 
@@ -87,35 +88,37 @@
         - you install also things that may be already installed
         - therefore, probably more disk space is needed
 
-#### Singularity
+### Singularity
+
+See [the UPPMAX Singularity user guide](../cluster_guides/singularity.md)
 
-- [Singularity user guide](../cluster_guides/singularity.md)
+### Docker
 
-#### Docker
-- Docker will unfortunately not work on the clusters, since it requires root permission.
+Docker will unfortunately not work on the clusters, since it requires root permission.
 
 !!! info "More info"
 
     - [Singularity user guide](../software/singularity.md)
     - [Part from Bianca course but applicable also on Rackham](https://github.com/UPPMAX/bianca_workshop/blob/main/docs/extra/containers.md)
 
-### Spack
+## Spack
 
 - The UPPMAX staff has already other ways to install most software applications.
 - Please use Spack only if other ways to install your tool is not possible or very difficult, e.g. requiring very many dependencies and it is not available through, e.g. Easybuild.
 - [UPPMAX Spack user guide](../software/spack.md)
 
-### Own development...
+## Own development
 
 - You may have your own code that you want to run on UPPMAX.
 - [Guide for compiling **serial** programs](compiling_serial.md)
 - [Guide for compiling **parallel** programs](compiling_parallel.md)
-    - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
+  - [Available **combinations** of compilers and parallel libraries](compiling_parallel.md#overview-of-available-compilers-from-gcc-and-intel-and-compatible-mpi-libraries)
 - [User guide for debuggers](../cluster_guides/debuggers.md)
 - [User guide for profilers](../cluster_guides/profilers.md)
 
 ## Run own scripts or programs
-- Unless your script or program is in the active path, you run it by the full path or `./<file>` if you are in the present directory.
+
+Unless your script or program is in the active path, you run it by the full path or `./<file>` if you are in the present directory.
 
 ## Summary
 

docs/cluster_guides/lftp_with_bianca.md

@@ -11,17 +11,17 @@ until it's really required unless you end your connect URL with a path.
 [When inside of SUNET](../getting_started/get_inside_sunet.md)
 (which can be on a local computer or on [Rackham](rackham.md)) do:
 
-```
+```bash
 lftp sftp://[user_name]-[project_id]@bianca-sftp.uppmax.uu.se/[user_name]-[project_id]/
 ```
 
 where
 
- * `[project_id]` is the ID of your [NAISS project](../getting_started/project.md)
- * `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md)
+- `[project_id]` is the ID of your [NAISS project](../getting_started/project.md)
+- `[user_name]` is the name of your [UPPMAX user account](../getting_started/user_account.md)
 
 For example:
 
-```
+```bash
 lftp sftp://[email protected]/sven-sens2016001/
 ```

docs/cluster_guides/login_transit.md

@@ -18,13 +18,13 @@ Below is a step-by-step procedure to login to [Transit](../cluster_guides/transi
 
 On your local computer, start a terminal and use [`ssh`](../software/ssh.md) to login to Transit:
 
-```
+```bash
 ssh [username]@transit.uppmax.uu.se
 ```
 
 where `[username]` is your UPPMAX username, for example:
 
-```
+```bash
 ssh [email protected]
 ```
 
@@ -38,8 +38,8 @@ it to your list of known hosts. Type `yes`.
     This is how it looks like when you are asked
     for adding Transit to your list of known hosts.
 
-    ![](./img/transit_add_to_known_hosts.png)
+    ![Transit is added to your list of known hosts](./img/transit_add_to_known_hosts.png)
 
 You are now logged in to Transit!
 
-![](./img/logged_in_transit.png)
+![Logged in to Transit](./img/logged_in_transit.png)