diff --git a/README.md b/README.md index 0c571d1..b3e7e5e 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ This tutorials aim to illustrate the process of **setting up a simulation** syst git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup ``` *** diff --git a/binder/environment.yml b/binder/environment.yml index a8f222e..58cff95 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -1,4 +1,4 @@ -name: biobb_AMBER_MDsetup_tutorials +name: biobb_wf_amber_md_setup channels: - conda-forge - bioconda diff --git a/biobb_wf_amber_md_setup/docs/source/abcsetup_tutorial.md b/biobb_wf_amber_md_setup/docs/source/abcsetup_tutorial.md index 4a08228..f98af77 100644 --- a/biobb_wf_amber_md_setup/docs/source/abcsetup_tutorial.md +++ b/biobb_wf_amber_md_setup/docs/source/abcsetup_tutorial.md @@ -41,7 +41,7 @@ The main **steps of the pipeline** are: git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup jupyter-notebook biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb ``` @@ -155,7 +155,7 @@ Model **DNA 3D structure** from a **nucleotide sequence** using the **nab tool** ```python # uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below: # import os -# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_AMBER_MDsetup_tutorials" # when running in Jupyter Notebook / Lab +# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber_md_setup" # when running in Jupyter Notebook / Lab # os.environ['AMBERHOME'] = "/usr/local" # when running in Google Colab ``` diff --git a/biobb_wf_amber_md_setup/docs/source/mdsetup_lig_tutorial.md b/biobb_wf_amber_md_setup/docs/source/mdsetup_lig_tutorial.md index 981bdc2..855fdd3 100644 --- a/biobb_wf_amber_md_setup/docs/source/mdsetup_lig_tutorial.md +++ b/biobb_wf_amber_md_setup/docs/source/mdsetup_lig_tutorial.md @@ -31,7 +31,7 @@ This tutorial aims to illustrate the process of **setting up a simulation system git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb ``` diff --git a/biobb_wf_amber_md_setup/docs/source/mdsetup_ph_tutorial.md b/biobb_wf_amber_md_setup/docs/source/mdsetup_ph_tutorial.md index ee71a40..ce62c8e 100644 --- a/biobb_wf_amber_md_setup/docs/source/mdsetup_ph_tutorial.md +++ b/biobb_wf_amber_md_setup/docs/source/mdsetup_ph_tutorial.md @@ -30,7 +30,7 @@ This tutorial aims to illustrate the process of **setting up a simulation system git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb ``` diff --git a/biobb_wf_amber_md_setup/docs/source/mdsetup_tutorial.md b/biobb_wf_amber_md_setup/docs/source/mdsetup_tutorial.md index 7da24de..bdd5f1a 100644 --- a/biobb_wf_amber_md_setup/docs/source/mdsetup_tutorial.md +++ b/biobb_wf_amber_md_setup/docs/source/mdsetup_tutorial.md @@ -29,7 +29,7 @@ This tutorial aims to illustrate the process of **setting up a simulation system git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb ``` diff --git a/biobb_wf_amber_md_setup/docs/source/readme.md b/biobb_wf_amber_md_setup/docs/source/readme.md index 0c571d1..b3e7e5e 100644 --- a/biobb_wf_amber_md_setup/docs/source/readme.md +++ b/biobb_wf_amber_md_setup/docs/source/readme.md @@ -35,7 +35,7 @@ This tutorials aim to illustrate the process of **setting up a simulation** syst git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git cd biobb_wf_amber_md_setup conda env create -f conda_env/environment.yml -conda activate biobb_AMBER_MDsetup_tutorials +conda activate biobb_wf_amber_md_setup ``` *** diff --git a/biobb_wf_amber_md_setup/html/abcsetup/biobb_amber_ABC_setup.web.html b/biobb_wf_amber_md_setup/html/abcsetup/biobb_amber_ABC_setup.web.html index c181646..2492a42 100644 --- a/biobb_wf_amber_md_setup/html/abcsetup/biobb_amber_ABC_setup.web.html +++ b/biobb_wf_amber_md_setup/html/abcsetup/biobb_amber_ABC_setup.web.html @@ -7546,7 +7546,7 @@
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
cd biobb_wf_amber_md_setup
conda env create -f conda_env/environment.yml
-conda activate biobb_AMBER_MDsetup_tutorials
+conda activate biobb_wf_amber_md_setup
jupyter-notebook biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb
# uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below:
# import os
-# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_AMBER_MDsetup_tutorials" # when running in Jupyter Notebook / Lab
+# os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber_md_setup" # when running in Jupyter Notebook / Lab
# os.environ['AMBERHOME'] = "/usr/local" # when running in Google Colab
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
cd biobb_wf_amber_md_setup
conda env create -f conda_env/environment.yml
-conda activate biobb_AMBER_MDsetup_tutorials
+conda activate biobb_wf_amber_md_setup
jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
cd biobb_wf_amber_md_setup
conda env create -f conda_env/environment.yml
-conda activate biobb_AMBER_MDsetup_tutorials
+conda activate biobb_wf_amber_md_setup
jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb
git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
cd biobb_wf_amber_md_setup
conda env create -f conda_env/environment.yml
-conda activate biobb_AMBER_MDsetup_tutorials
+conda activate biobb_wf_amber_md_setup
jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb