diff --git a/biobb_wf_amber_abc_setup/docker/README.md b/biobb_wf_amber_abc_setup/docker/README.md index 4c8dc85..6ec8622 100644 --- a/biobb_wf_amber_abc_setup/docker/README.md +++ b/biobb_wf_amber_abc_setup/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :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. + #### 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 -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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_amber_md_setup/docker/README.md b/biobb_wf_amber_md_setup/docker/README.md index 472963d..5058a69 100644 --- a/biobb_wf_amber_md_setup/docker/README.md +++ b/biobb_wf_amber_md_setup/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :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. + #### 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 -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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_amber_md_setup_lig/docker/README.md b/biobb_wf_amber_md_setup_lig/docker/README.md index 85c1f33..c0b8b23 100644 --- a/biobb_wf_amber_md_setup_lig/docker/README.md +++ b/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 ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :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. + #### 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 -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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_cmip/docker/README.md b/biobb_wf_cmip/docker/README.md index 62af105..e82e89e 100644 --- a/biobb_wf_cmip/docker/README.md +++ b/biobb_wf_cmip/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :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. + #### 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 -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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_dna_helparms/docker/README.md b/biobb_wf_dna_helparms/docker/README.md index bd6d7d4..026f1fc 100644 --- a/biobb_wf_dna_helparms/docker/README.md +++ b/biobb_wf_dna_helparms/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_dna_helparms + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_dna_helparms + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_flexdyn/docker/README.md b/biobb_wf_flexdyn/docker/README.md index ff7c819..4ffe9c5 100644 --- a/biobb_wf_flexdyn/docker/README.md +++ b/biobb_wf_flexdyn/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_flexdyn + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_flexdyn + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_flexserv/docker/README.md b/biobb_wf_flexserv/docker/README.md index e7de952..e32aac4 100644 --- a/biobb_wf_flexserv/docker/README.md +++ b/biobb_wf_flexserv/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_flexserv + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_flexserv + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_godmd/docker/README.md b/biobb_wf_godmd/docker/README.md index 76f5f10..e752955 100644 --- a/biobb_wf_godmd/docker/README.md +++ b/biobb_wf_godmd/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_godmd + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_godmd + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_ligand_parameterization/docker/README.md b/biobb_wf_ligand_parameterization/docker/README.md index df5af16..2e309f5 100644 --- a/biobb_wf_ligand_parameterization/docker/README.md +++ b/biobb_wf_ligand_parameterization/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_ligand_parameterization + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_ligand_parameterization + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_md_setup/docker/README.md b/biobb_wf_md_setup/docker/README.md index bc89803..46e811b 100644 --- a/biobb_wf_md_setup/docker/README.md +++ b/biobb_wf_md_setup/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_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. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_md_setup_mutations/docker/README.md b/biobb_wf_md_setup_mutations/docker/README.md index 5b311be..655a69c 100644 --- a/biobb_wf_md_setup_mutations/docker/README.md +++ b/biobb_wf_md_setup_mutations/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## Download and execute container from docker hub @@ -39,6 +39,12 @@ 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_md_setup_mutations + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## Build container in house To execute the workflow through a docker container, please follow the next steps: @@ -77,6 +83,12 @@ 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_pmx_tutorial/docker/README.md b/biobb_wf_pmx_tutorial/docker/README.md index 84bcfee..c3e8f7e 100644 --- a/biobb_wf_pmx_tutorial/docker/README.md +++ b/biobb_wf_pmx_tutorial/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_pmx_tutorial + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_pmx_tutorial + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_protein-complex_md_setup/docker/README.md b/biobb_wf_protein-complex_md_setup/docker/README.md index 281ab40..9461042 100644 --- a/biobb_wf_protein-complex_md_setup/docker/README.md +++ b/biobb_wf_protein-complex_md_setup/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_protein-complex_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. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_protein-complex_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. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_protein_md_analysis/docker/README.md b/biobb_wf_protein_md_analysis/docker/README.md index ffb03bc..d26bb1f 100644 --- a/biobb_wf_protein_md_analysis/docker/README.md +++ b/biobb_wf_protein_md_analysis/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## Download and execute container from docker hub @@ -39,6 +39,12 @@ 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_protein_md_analysis + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## Build container in house To execute the workflow through a docker container, please follow the next steps: @@ -77,6 +83,12 @@ 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_structure_checking/docker/README.md b/biobb_wf_structure_checking/docker/README.md index 0990b63..53f6451 100644 --- a/biobb_wf_structure_checking/docker/README.md +++ b/biobb_wf_structure_checking/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_structure_checking + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_structure_checking + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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. diff --git a/biobb_wf_virtual-screening_fpocket/docker/README.md b/biobb_wf_virtual-screening_fpocket/docker/README.md index 3e1f9fb..950e5b8 100644 --- a/biobb_wf_virtual-screening_fpocket/docker/README.md +++ b/biobb_wf_virtual-screening_fpocket/docker/README.md @@ -4,7 +4,7 @@ All the **BioBB workflows** can be executed via **docker container**. Inside thi ## 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. ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data biobb/biobb_wf_virtual-screening_fpocket + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data biobb/biobb_wf_virtual-screening_fpocket + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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 -d -e MODE=jupyter -e USER_JN=custom.ipynb -p :8888 -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new Jupyter Notebook file **must fulfill** the same **specifications** as the original one. + #### 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 -e USER_PY=custom.py -v /path/to/inputs:/data + +Take into account that the **dependencies are not customisable**, so this new workflow file **must fulfill** the same **specifications** as the original one. + ## 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.