Unifying workflow name

bioexcel · May 31, 2024 · 5d46bc8 · 5d46bc8
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -7546,7 +7546,7 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
 <span class="go">cd biobb_wf_amber_md_setup</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_AMBER_MDsetup_tutorials</span>
+<span class="go">conda activate biobb_wf_amber_md_setup</span>
 <span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb</span>
 </pre></div>
 <hr/>
@@ -7736,7 +7736,7 @@ <h2 id="Model-DNA-3D-structure">Model DNA 3D structure<a class="anchor-link" hre
 <div class="cm-editor cm-s-jupyter">
 <div class="highlight hl-ipython3"><pre><span></span><span class="c1"># uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below:</span>
 <span class="c1"># import os</span>
-<span class="c1"># os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_AMBER_MDsetup_tutorials" # when running in Jupyter Notebook / Lab</span>
+<span class="c1"># os.environ['AMBERHOME'] = "/path/to/anaconda3/envs/biobb_wf_amber_md_setup" # when running in Jupyter Notebook / Lab</span>
 <span class="c1"># os.environ['AMBERHOME'] = "/usr/local" # when running in Google Colab</span>
 </pre></div>
 </div>

diff --git a/biobb_wf_amber_md_setup/html/mdsetup/biobb_amber_setup_notebook.web.html b/biobb_wf_amber_md_setup/html/mdsetup/biobb_amber_setup_notebook.web.html
@@ -7536,7 +7536,7 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
 <span class="go">cd biobb_wf_amber_md_setup</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_AMBER_MDsetup_tutorials</span>
+<span class="go">conda activate biobb_wf_amber_md_setup</span>
 <span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb</span>
 </pre></div>
 <hr/>

diff --git a/biobb_wf_amber_md_setup/html/mdsetup_lig/biobb_amber_complex_setup_notebook.web.html b/biobb_wf_amber_md_setup/html/mdsetup_lig/biobb_amber_complex_setup_notebook.web.html
@@ -7538,7 +7538,7 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
 <span class="go">cd biobb_wf_amber_md_setup</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_AMBER_MDsetup_tutorials</span>
+<span class="go">conda activate biobb_wf_amber_md_setup</span>
 <span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb</span>
 </pre></div>
 <hr/>

diff --git a/biobb_wf_amber_md_setup/html/mdsetup_ph/biobb_amber_CpHMD_notebook.web.html b/biobb_wf_amber_md_setup/html/mdsetup_ph/biobb_amber_CpHMD_notebook.web.html
@@ -7540,7 +7540,7 @@ <h3 id="Auxiliary-libraries-used">Auxiliary libraries used<a class="anchor-link"
 <h3 id="Conda-Installation">Conda Installation<a class="anchor-link" href="#Conda-Installation">¶</a></h3><div class="highlight"><pre><span></span><span class="go">git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git</span>
 <span class="go">cd biobb_wf_amber_md_setup</span>
 <span class="go">conda env create -f conda_env/environment.yml</span>
-<span class="go">conda activate biobb_AMBER_MDsetup_tutorials</span>
+<span class="go">conda activate biobb_wf_amber_md_setup</span>
 <span class="go">jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb</span>
 </pre></div>
 <hr/>

diff --git a/biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb b/biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb
@@ -47,7 +47,7 @@
     "git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git\n",
     "cd biobb_wf_amber_md_setup\n",
     "conda env create -f conda_env/environment.yml\n",
-    "conda activate biobb_AMBER_MDsetup_tutorials\n",
+    "conda activate biobb_wf_amber_md_setup\n",
     "jupyter-notebook biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb\n",
     "```\n",
     "\n",
@@ -204,7 +204,7 @@
    "source": [
     "# uncomment in case of experiencing issues with undefined AMBERHOME variable in the cell below:\n",
     "# import os\n",
-    "# os.environ['AMBERHOME'] = \"/path/to/anaconda3/envs/biobb_AMBER_MDsetup_tutorials\" # when running in Jupyter Notebook / Lab\n",
+    "# os.environ['AMBERHOME'] = \"/path/to/anaconda3/envs/biobb_wf_amber_md_setup\" # when running in Jupyter Notebook / Lab\n",
     "# os.environ['AMBERHOME'] = \"/usr/local\" # when running in Google Colab"
    ]
   },

diff --git a/biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb b/biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb
@@ -35,7 +35,7 @@
     "git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git\n",
     "cd biobb_wf_amber_md_setup\n",
     "conda env create -f conda_env/environment.yml\n",
-    "conda activate biobb_AMBER_MDsetup_tutorials\n",
+    "conda activate biobb_wf_amber_md_setup\n",
     "jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup/biobb_amber_setup_notebook.ipynb\n",
     "```\n",
     "\n",
@@ -1634,7 +1634,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.8.9"
   },
   "vscode": {
    "interpreter": {

diff --git a/biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb b/biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb
@@ -37,7 +37,7 @@
     "git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git\n",
     "cd biobb_wf_amber_md_setup\n",
     "conda env create -f conda_env/environment.yml\n",
-    "conda activate biobb_AMBER_MDsetup_tutorials\n",
+    "conda activate biobb_wf_amber_md_setup\n",
     "jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_lig/biobb_amber_complex_setup_notebook.ipynb\n",
     "```\n",
     "\n",

diff --git a/biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb b/biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb
@@ -36,7 +36,7 @@
     "git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git\n",
     "cd biobb_wf_amber_md_setup\n",
     "conda env create -f conda_env/environment.yml\n",
-    "conda activate biobb_AMBER_MDsetup_tutorials\n",
+    "conda activate biobb_wf_amber_md_setup\n",
     "jupyter-notebook biobb_wf_amber_md_setup/notebooks/mdsetup_ph/biobb_amber_CpHMD_notebook.ipynb\n",
     "```\n",
     "\n",

diff --git a/conda_env/environment.yml b/conda_env/environment.yml
@@ -1,4 +1,4 @@
-name: biobb_AMBER_MDsetup_tutorials
+name: biobb_wf_amber_md_setup
 channels:
   - conda-forge
   - bioconda