Update biobb_all 2025.1 environment

Author: RubenChM

biobb/README.md

@@ -12,6 +12,11 @@ git submodule foreach --recursive 'git checkout YOUR_TAG_NAME || true'
 To update the submodules to the last tagged version:
 ```bash
 git submodule foreach --recursive 'git checkout $(git tag --sort=-v:refname | head -n 1)'
+
+```
+ To attach to the HEAD:
+```bash
+git submodule foreach --recursive 'git checkout HEAD'
 ```
 
 To pull while cloning the repository:
@@ -21,7 +26,7 @@ git clone --recurse-submodules https://github.com/bioexcel/biobb.git
 
 To pull after cloning:
 ```bash
-git submodule update --remote --merge --recursive
+git submodule update --init --remote --recursive
 ```
 
 # Conda Environment Setup for BioBB

biobb/biobb_all.yml

@@ -3,14 +3,15 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - biobb_adapters==5.1.2
   - biobb_amber==5.1.0
   - biobb_analysis==5.1.1
   - biobb_chemistry==5.1.0
   - biobb_cmip==5.1.0
   - biobb_cp2k==5.1.0
   - biobb_dna==5.1.0
   - biobb_flexdyn==5.1.0
-  - biobb_flexserv==5.1.0
+  - biobb_flexserv==5.1.0=*_1
   - biobb_godmd==5.1.1
   - biobb_gromacs==5.1.1
   - biobb_haddock==5.1.0
@@ -19,9 +20,8 @@ dependencies:
   - biobb_model==5.1.0
   - biobb_pdb_tools==5.1.0
   - biobb_pmx==5.1.0
-  - biobb_pytorch==5.1.0  # Can be remove to make the environment lighter
+  #- biobb_pytorch==5.1.0  # Can be remove to make the environment lighter
   - biobb_structure_utils==5.1.0
   - biobb_vs==5.1.0
-  - biobb_adapters==5.1.0
   - conda-pack