Merge branch 'main' of github.com:bioexcel/biobb_workflows

biobb_wf_amber_abc_setup/docker/README.md

@@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi
 
 ## <a name="requirements"></a>Requirements
 
-For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fullfilled, you will be able to install the workflow.
+For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fulfilled, you will be able to install the workflow.
 
 ## <a name="download"></a>Download and execute container from docker hub
 
@@ -41,6 +41,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data biobb/biobb_wf_amber_abc_setup
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-d"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -56,6 +62,12 @@ Where:
 * **container_name** is the name of the container (optional).
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_amber_abc_setup
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="build"></a>Build container in house
 
 To execute the workflow through a docker container, please follow the next steps:
@@ -96,6 +108,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-b"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -112,6 +130,12 @@ Where:
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 * **container_image** is the name of the docker container image.
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="time"></a>Time of execution
 
 Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a **few minutes** to **several hours**. The workflow progress will be shown in your terminal if you execute the workflow via python.

biobb_wf_amber_md_setup/docker/README.md

@@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi
 
 ## <a name="requirements"></a>Requirements
 
-For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fullfilled, you will be able to install the workflow.
+For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fulfilled, you will be able to install the workflow.
 
 ## <a name="download"></a>Download and execute container from docker hub
 
@@ -41,6 +41,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data biobb/biobb_wf_amber_md_setup
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-d"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -56,6 +62,12 @@ Where:
 * **container_name** is the name of the container (optional).
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_amber_md_setup
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="build"></a>Build container in house
 
 To execute the workflow through a docker container, please follow the next steps:
@@ -96,6 +108,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-b"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -112,6 +130,12 @@ Where:
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 * **container_image** is the name of the docker container image.
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="time"></a>Time of execution
 
 Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a **few minutes** to **several hours**. The workflow progress will be shown in your terminal if you execute the workflow via python.

biobb_wf_amber_md_setup_lig/docker/README.md

@@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi
 
 ## <a name="requirements"></a>Requirements
 
-For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fullfilled, you will be able to install the workflow.
+For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fulfilled, you will be able to install the workflow.
 
 ## <a name="download"></a>Download and execute container from docker hub
 
@@ -41,6 +41,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data biobb/biobb_wf_amber_md_setup_lig
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-d"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -56,6 +62,12 @@ Where:
 * **container_name** is the name of the container (optional).
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_amber_md_setup_lig
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="build"></a>Build container in house
 
 To execute the workflow through a docker container, please follow the next steps:
@@ -96,6 +108,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-b"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -112,6 +130,12 @@ Where:
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 * **container_image** is the name of the docker container image.
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="time"></a>Time of execution
 
 Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a **few minutes** to **several hours**. The workflow progress will be shown in your terminal if you execute the workflow via python.

biobb_wf_cmip/docker/README.md

@@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi
 
 ## <a name="requirements"></a>Requirements
 
-For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fullfilled, you will be able to install the workflow.
+For executing this **BioBB workflow**, there is a single requirement: to have [**Docker**](https://docs.docker.com/engine/install/) installed in your computer. Once this requirement is fulfilled, you will be able to install the workflow.
 
 ## <a name="download"></a>Download and execute container from docker hub
 
@@ -41,6 +41,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data biobb/biobb_wf_cmip
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-d"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -56,6 +62,12 @@ Where:
 * **container_name** is the name of the container (optional).
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_cmip
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="build"></a>Build container in house
 
 To execute the workflow through a docker container, please follow the next steps:
@@ -96,6 +108,12 @@ This instruction will run the container in **detached** (or background) mode, so
 
 Note that **the port can change** depending on the value provided in the previous step.
 
+For **running** the container with a **custom Jupyter Notebook**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -d -e MODE=jupyter -e USER_JN=custom.ipynb -p <port>:8888 -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one.
+
 #### <a name="run-py-b"></a>Run in Python
 
 Below you can find the list of all the needed **files** for executing this workflow in **python**:
@@ -112,6 +130,12 @@ Where:
 * **/path/to/inputs** is the path to the folder where the **input(s)** and **workflow.yml** files are located (all of them must be in the same folder).
 * **container_image** is the name of the docker container image.
 
+For **running** the container with a **custom workflow file**, please locate this file in the **same folder** where the inputs are and then type the following instruction in your **terminal**:
+
+    docker run --name <container_name> -e USER_PY=custom.py -v /path/to/inputs:/data <container_image>
+
+Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one.
+
 ## <a name="time"></a>Time of execution
 
 Take into account that depending on the number of steps, the tools executed and the settings provided, along with the power of your computer, the execution of the workflow can take from a **few minutes** to **several hours**. The workflow progress will be shown in your terminal if you execute the workflow via python.