FIX: use shell instead of bash

README.md

@@ -4,20 +4,24 @@
 
 ## How to use on Merlin systems (Merlin6/Merlin7)
 
-0. Load the spack module:
+Load the spack module
 
-```bash
+```shell
 [stable] user@login001:~> module load spack
 ```
-+ If you want to use the unstable software stack do in addition:
 
-```bash
+Voilà you're done you can use Spack! :)
+
++ Side note: the default software stack loaded for you is stable, which might not contain all the packages you're looking for, </br>
+so if you want to use the unstable software stack switch to it using:
+
+```shell
 spack env activate -p unstable
 ```
 
-### Find out what's already installed
+## Find out what's already installed
 
-```bash
+```shell
 [unstable] user@login001:~>  spack find
 ==> In environment unstable
 ==> 1 root specs
@@ -121,13 +125,13 @@ rrfdppp py-alphafold@2.3.2~cuda build_system=python_pip  tqziprv py-alphafold@2.
 As you can see there are two installation of py-alphafold, one with +cuda and one without. </br>
 In this particular example, there is only one variant that interests you, so you can do:
 
-``` bash
+``` shell
 spack load py-alphafold +cuda
 ```
 
 However if multiple variants are interesting to you and you don't want to have to cite all of them you can do:
 
-``` bash
+``` shell
 spack load /tqziprv # refer to the installation with its hash directly.
 ```
 
@@ -136,19 +140,19 @@ spack load /tqziprv # refer to the installation with its hash directly.
 1. Check if your package is already implemented in Spack. <br/>
  You can also use the following website: https://packages.spack.io/
 
-```bash
+```shell
 spack list $pkg_name # e.g opal
 ```
 
 2. Check the package variants you want to set e.g +cuda +openmp ^openmpi ...
 
-```bash
+```shell
 spack info $pkg_name # e.g opal
 ```
 
 3. Add your package to your personal environment
 
-```bash
+```shell
 spack add $pkg_name@version +variant1 ^dep1@version1
 ```
 
@@ -156,31 +160,31 @@ spack add $pkg_name@version +variant1 ^dep1@version1
 /afs/psi.ch/sys/spack/user/$USER/spack-environment/$pkg_name <br/>
 and tell Spack you want to use it using:
 
-```bash
+```shell
 spack develop $pkg_name@version # Skip this if you don't want to develop from local source
 ```
 4. Check the whole dependency tree of your spec and <br/>
 if you don't need to set more variants
 
-```bash
+```shell
 spack concretize
 ```
 
 5. Install the packages in your environment
 
-```bash
+```shell
 spack install # -v for verbose
 ```
 
 6. Load your package
 
-```bash
+```shell
 spack load $pkg_name@version +variant1 ^dep1@version1
 ```
 
 7. Submit your script
 
-```bash
+```shell
 sbatch batch.script
 ```
 ### Switching between environments
@@ -189,7 +193,7 @@ There are two environment available to users; stable and unstable. <br/>
 The first one is loaded by default when loading the module. <br/>
 If you want to switch between the two and use different software stack you can use the following command:
 
-```bash
+```shell
 spack env activate -p unstable # or stable
 ```
 
@@ -197,13 +201,13 @@ spack env activate -p unstable # or stable
 
 When adding the following command you actually add a package to your own software stack;
 
-```bash
+```shell
 spack add $pkg_name@version +variant1 ^dep1@version1
 ```
 
 You can check which package will be concretized and are in your environment using;
 
-```bash
+```shell
 [unstable] user@login001:~> spack find
 ==> In environment unstable
 ==> 1 root specs
@@ -230,13 +234,13 @@ The installed packages are either packages that were previously installed by adm
 
 If you want to remove this package from your personal env, you can use the following command: <br/>
 
-```bash
+```shell
 spack rm $pkg_name@version +variant1 ^dep1@version1
 ```
 
 or
 
-```bash
+```shell
 [stable] user@login001:~> spack config edit
 spack:
   ...
@@ -251,7 +255,7 @@ and remove it manually from the spec list.
 
 ### Install Spack
 
-```bash
+```shell
 user@supersystem:~> cd /scratch/$USER
 
 user@supersystem:~> git clone -c feature.manyFiles=true https://github.com/spack/spack.git