Fix markdown style issues

docs/software/gromacs.md

@@ -4,8 +4,6 @@ This page describes how to run the GROMACS molecular dynamics software on UPPMAX
 
 Have a look on this page as well - [best practices](https://docs.bioexcel.eu/gromacs_bpg/en/master/cookbook/cookbook.html) running GROMAC on HPC.
 
-
-
 Selected setups for benchmarking on HPC2N as [examples](https://github.com/hpc2n/CourseEfficientMD/tree/main/benchmark/GROMACS).
 
 ## Loading the gromac module
@@ -52,9 +50,12 @@ $MPIRUN $GMX mdrun $ntmpi -ntomp $ntomp -s MEM.tpr -nsteps 10000 -resethway
 ```
 
 ## How important is to select appropriate options
-Here is a simple benchmark ran on single interactive node with 20CPUs using  the MEM example from this benchmark https://www.mpibpc.mpg.de/grubmueller/bench.
 
-``` bash
+Here is a simple benchmark ran on single interactive node with 20CPUs
+using the MEM example from
+[this benchmark](https://www.mpibpc.mpg.de/grubmueller/bench):
+
+```bash
 $ module load gromacs/2021.1.th
 $ mpirun -np XX gmx_mpi mdrun -ntomp YY -s MEM.tpr -nsteps 10000 -resethway
 ```
@@ -91,25 +92,32 @@ md.log:Performance:        2.012       11.931
 ```
 
 Notice how bad is the last run
+
 `$ mpirun -np 1 gmx_mpi mdrun -ntomp 20 -s MEM.tpr -nsteps 10000 -resethway` (lines 25-26)
 
 According to this short test, this particular setup runs best on single Rackham node with
+
 `$ mpirun -np 10 gmx_mpi mdrun -ntomp 2 -s MEM.tpr -nsteps 10000 -resethway` (lines 8-10)
 
 
 ## Running older versions of gromacs
 
-### Versions 4.5.1 to 5.0.4:
+### Versions 4.5.1 to 5.0.4
+
 The gromacs tools have been compiled serially. The mdrun program has also been compiled in parallel using MPI. The name of the parallel binary is mdrun_mpi.
 
 Run the parallelized program using:
+
 ``` bash
 mpirun -np XXX mdrun_mpi
 ```
+
 ... where XXX is the number of cores to run the program on.
 
 ### Version 5.1.1
+
 The binary is gmx_mpi and (e.g.) the mdrun command is issued like this:
+
 ``` bash
 mpirun -np XXX gmx_mpi mdrun
 ```

docs/software/ides.md

@@ -1,6 +1,6 @@
 # IDE:s
 
-![](../cluster_guides/img/rstudio_in_action_480_x_270.png)
+![RStudio on Bianca](../cluster_guides/img/rstudio_in_action_480_x_270.png)
 
 > RStudio is an IDEs. Here, it is run on Bianca.
 
@@ -17,7 +17,7 @@ language (e.g. RStudio) and some allow multiple programming languages.
 
 How to use an IDE depends on the UPPMAX cluster you want to use:
 
- * [IDEs on Bianca](../cluster_guides/ides_on_bianca.md)
- * [IDEs on Rackham](../cluster_guides/ides_on_rackham.md)
+- [IDEs on Bianca](../cluster_guides/ides_on_bianca.md)
+- [IDEs on Rackham](../cluster_guides/ides_on_rackham.md)
 
 In general, using an IDE is easiest on Rackham and hardest on Bianca.

docs/software/igv.md

@@ -6,27 +6,29 @@ This guide will go through step by step how to start Integrative Genomics Viewer
 
 In a terminal, use [SSH with X forwarding enabled](../software/ssh_x_forwarding.md):
 
-```console
+```bash
 ssh -X [user name]@rackham.uppmax.uu.se
 ```
 
 For example:
 
-```
+```bash
 ssh -X [email protected]
 ```
 
 - Windows users: we recommend the [SSH client](../software/ssh_client.md) MobaXterm
 - MacOS users: the built-in [SSH client](../software/ssh_client.md) `ssh` does need [XQuartz](https://www.xquartz.org/) installed too
 
 ## Step 2: Reserve a node using "interactive"
+
 Since genomic sequences require lots of memory, it is not suitable to run IGV on one of the login nodes. That would slow down the response times for all other users on the same login node..
 
 Instead, reserve a node that you will have all by yourself. This command will reserve a whole node for 12 hours, the maximum amount of interactive time you can get and still receive a high priority for your job (feel free to change that if you want to).
 
 ```console
 interactive -A [UPPMAX project id] -p node -t 12:00:00
 ```
+
 For example:
 
 ```console
@@ -40,16 +42,19 @@ interactive -A snic2017-7-274 -M snowy -p node -t\ 12:00:00
 ```
 
 ## Step 3: Load the IGV module
+
 When your job has been started, type the following command to load the IGV module:
 
 ```console
 module load bioinfo-tools IGV
 ```
 
 ## Step 4: Start IGV
+
 To start IGV, type the following:
 
 ```console
 igv-node
 ```
+
 That's it, now IGV should be loaded and ready to go. For more information about how to use IGV, please visit [IGV's user guide](https://igv.org/doc/desktop/).