# HPC/Exascale Centre of Excellence in Personalised Medicine
## Base Building Block
This package provides the base for all **Building Blocks (BBs)** developed in the **HPC/Exascale Centre of Excellence in Personalised Medicine** ([PerMedCoE](https://permedcoe.eu/)) project.
## Table of Contents
- [HPC/Exascale Centre of Excellence in Personalised Medicine](#hpcexascale-centre-of-excellence-in-personalised-medicine)
- [Base Building Block](#base-building-block)
- [Table of Contents](#table-of-contents)
- [User instructions](#user-instructions)
- [Requirements](#requirements)
- [Installation](#installation)
- [Command line](#command-line)
- [Option execute:](#option-execute)
- [Option template:](#option-template)
- [Option deploy:](#option-deploy)
- [Public API](#public-api)
- [Uninstall](#uninstall)
- [Developer instructions](#developer-instructions)
- [Building block](#building-block)
- [License](#license)
- [Contact](#contact)
## User instructions
### Requirements
- Python >= 3.6
- [Singularity](https://singularity.lbl.gov/docs-installation)
### Installation
There are two ways to install this package (from Pypi and manually):
- From Pypi:
This package is publicly available in Pypi:
```shell
pip install permedcoe
```
or more specifically:
```shell
python3 -m pip install permedcoe
```
- From source code:
This package provides an automatic installation script:
```shell
./install.sh
```
### Command line
This package provides the `permedcoe` command:
```shell
$ permedcoe -h
usage: permedcoe [-h] [-d] [-l {debug,info,warning,error,critical}]
{execute,x,template,t,deploy,d} ...
positional arguments:
{execute,x,template,t,deploy,d}
execute (x) Execute a building block.
template (t) Shows an example of the requested template.
deploy (d) Download and deploy the requested workflow or building block.
options:
-h, --help show this help message and exit
-d, --debug Enable debug mode. Overrides log_level (default: False)
-l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}
Set logging level. (default: error)
```
#### Option execute:
- It enables to execute single building blocks or applications:
```shell
$ permedcoe execute -h
usage: permedcoe execute [-h] {building_block,bb,application,app} ...
positional arguments:
{building_block,bb,application,app}
building_block (bb)
Execute a building block.
application (app) Execute an application.
optional arguments:
-h, --help show this help message and exit
```
- In particular for building blocks:
```shell
$ permedcoe execute building_block -h
usage: permedcoe execute building_block [-h] name [parameters ...]
positional arguments:
name Building Block to execute
parameters Building Block parameters (default: None)
options:
-h, --help show this help message and exit
```
Specifying the particular building block to execute (must be installed), provides more detailed information:
```shell
$ permedcoe execute building_block MaBoSS_BB -h
usage: permedcoe [-h] [-c CONFIG] [-d] [-l {debug,info,warning,error,critical}] [--tmpdir TMPDIR]
[--processes PROCESSES] [--gpus GPUS] [--memory MEMORY] [--mount_points MOUNT_POINTS]
{default,sensitivity} ...
This building block uses MaBoSS to screen all the possible knockouts of a given Boolean model. It
produces a candidate gene list formatted as a text file (single gene per row). More information on
MaBoSS can be found in [Stoll G. et al. (2017)](https://academic.oup.com/bioinformatics/article-
lookup/doi/10.1093/bioinformatics/btx123) and in the [MaBoSS GitHub
repository](https://github.com/maboss-bkmc/MaBoSS-env-2.0).
positional arguments:
{default,sensitivity}
options:
-h, --help show this help message and exit
-c CONFIG, --config CONFIG
(CONFIG) Configuration file path
-d, --debug Enable Building Block debug mode. Overrides log_level
-l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}
Set logging level
--tmpdir TMPDIR Temp directory to be mounted in the container
--processes PROCESSES
Number of processes for MPI executions
--gpus GPUS Requirements for GPU jobs
--memory MEMORY Memory requirement
--mount_points MOUNT_POINTS
Comma separated alias:folder to be mounted in the container
```
- In particular for building blocks:
```shell
$ permedcoe execute application -h
usage: permedcoe execute application [-h] [-w {none,pycompss,nextflow,snakemake}]
[-f FLAGS [FLAGS ...]]
name [parameters [parameters ...]]
positional arguments:
name Application to execute
parameters Application parameters (default: None)
optional arguments:
-h, --help show this help message and exit
-w {none,pycompss,nextflow,snakemake}, --workflow_manager {none,pycompss,nextflow,snakemake}
Workflow manager to use (default: none)
-f FLAGS [FLAGS ...], --flags FLAGS [FLAGS ...]
Workflow manager flags (default: None)
```
#### Option template:
- It available to create a skeleton of a building block or an application:
```shell
$ permedcoe template -h
usage: permedcoe template [-h] [-t {all,pycompss,nextflow,snakemake}]
{bb,building_block,app,application} name
positional arguments:
{bb,building_block,app,application}
Creates a Building Block or Application template.
name Building Block or Application name.
optional arguments:
-h, --help show this help message and exit
-t {all,pycompss,nextflow,snakemake}, --type {all,pycompss,nextflow,snakemake}
Application type. (default: all)
```
#### Option deploy:
- It available to deploy an existing Building Block or Workflow in a **local machine (e.g. laptop)**:
```shell
$ permedcoe deploy -h
usage: permedcoe deploy [-h] {building_block,bb,workflow,wf} ...
positional arguments:
{building_block,bb,workflow,wf}
building_block (bb)
A specific building block.
workflow (wf) A specific workflow.
options:
-h, --help show this help message and exit
```
For the deployment in supercomputers, please contact PerMedCoE: <https://permedcoe.eu/contact/>.
### Public API
The `permedcoe` package provides a set of public decorators, parameter type definition and functions to be used in the Building Block implementation.
- Public decorators:
```python
from permedcoe import container
from permedcoe import constraint
from permedcoe import binary
from permedcoe import mpi
from permedcoe import task
```
- Parameter type definition:
```python
from permedcoe import Type
from permedcoe import FILE_IN
from permedcoe import FILE_OUT
from permedcoe import FILE_INOUT
from permedcoe import DIRECTORY_IN
from permedcoe import DIRECTORY_OUT
from permedcoe import DIRECTORY_INOUT
from permedcoe import StdIOStream
from permedcoe import STDIN
from permedcoe import STDOUT
from permedcoe import STDERR
```
- Functions:
```python
from permedcoe import get_environment
from permedcoe import set_debug
from permedcoe import invoker
```
- Classes:
```python
from permedcoe import Arguments
```
### Uninstall
Uninstall can be done as usual `pip` packages:
There are two ways to uninstall this package, that depends on the way that it was installed (from Pypi or using `install.sh`):
- From Pypi:
```shell
pip uninstall permedcoe
```
or more specifically:
```shell
python3 -m pip uninstall permedcoe
```
- From manual installation (using `install.sh`):
```shell
./uninstall.sh
```
And then the folder can be cleaned as well using the `clean.sh` script.
```shell
./clean.sh
```
## Developer instructions
### Building block
If you are willing to implement your Building Block (BB), check the following repositories,
where you will find documentation, tutorials, and BB/application samples:
- [Documentation](https://permedcoe.readthedocs.io/en/latest/)
- [Tutorial](https://permedcoe.readthedocs.io/en/latest/04_creating/04_tutorial/tutorial.html)
- [basic_application](https://github.com/PerMedCoE/basic_application)
- [Lysozyme_in_water](https://github.com/PerMedCoE/Lysozyme_in_water)
## License
[Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)
## Contact
<https://permedcoe.eu/contact/>
This software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)).
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"description": "# HPC/Exascale Centre of Excellence in Personalised Medicine\n\n## Base Building Block\n\nThis package provides the base for all **Building Blocks (BBs)** developed in the **HPC/Exascale Centre of Excellence in Personalised Medicine** ([PerMedCoE](https://permedcoe.eu/)) project.\n\n## Table of Contents\n\n- [HPC/Exascale Centre of Excellence in Personalised Medicine](#hpcexascale-centre-of-excellence-in-personalised-medicine)\n - [Base Building Block](#base-building-block)\n - [Table of Contents](#table-of-contents)\n - [User instructions](#user-instructions)\n - [Requirements](#requirements)\n - [Installation](#installation)\n - [Command line](#command-line)\n - [Option execute:](#option-execute)\n - [Option template:](#option-template)\n - [Option deploy:](#option-deploy)\n - [Public API](#public-api)\n - [Uninstall](#uninstall)\n - [Developer instructions](#developer-instructions)\n - [Building block](#building-block)\n - [License](#license)\n - [Contact](#contact)\n\n## User instructions\n\n### Requirements\n\n- Python >= 3.6\n- [Singularity](https://singularity.lbl.gov/docs-installation)\n\n### Installation\n\nThere are two ways to install this package (from Pypi and manually):\n\n- From Pypi:\n\n This package is publicly available in Pypi:\n\n ```shell\n pip install permedcoe\n ```\n\n or more specifically:\n\n ```shell\n python3 -m pip install permedcoe\n ```\n\n- From source code:\n\n This package provides an automatic installation script:\n\n ```shell\n ./install.sh\n ```\n\n### Command line\n\n This package provides the `permedcoe` command:\n\n ```shell\n $ permedcoe -h\n usage: permedcoe [-h] [-d] [-l {debug,info,warning,error,critical}]\n {execute,x,template,t,deploy,d} ...\n\n positional arguments:\n {execute,x,template,t,deploy,d}\n execute (x) Execute a building block.\n template (t) Shows an example of the requested template.\n deploy (d) Download and deploy the requested workflow or building block.\n\n options:\n -h, --help show this help message and exit\n -d, --debug Enable debug mode. Overrides log_level (default: False)\n -l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}\n Set logging level. (default: error)\n ```\n#### Option execute:\n\n- It enables to execute single building blocks or applications:\n\n ```shell\n $ permedcoe execute -h\n usage: permedcoe execute [-h] {building_block,bb,application,app} ...\n\n positional arguments:\n {building_block,bb,application,app}\n building_block (bb)\n Execute a building block.\n application (app) Execute an application.\n\n optional arguments:\n -h, --help show this help message and exit\n ```\n\n - In particular for building blocks:\n\n ```shell\n $ permedcoe execute building_block -h\n usage: permedcoe execute building_block [-h] name [parameters ...]\n\n positional arguments:\n name Building Block to execute\n parameters Building Block parameters (default: None)\n\n options:\n -h, --help show this help message and exit\n ```\n\n Specifying the particular building block to execute (must be installed), provides more detailed information:\n\n ```shell\n $ permedcoe execute building_block MaBoSS_BB -h\n usage: permedcoe [-h] [-c CONFIG] [-d] [-l {debug,info,warning,error,critical}] [--tmpdir TMPDIR]\n [--processes PROCESSES] [--gpus GPUS] [--memory MEMORY] [--mount_points MOUNT_POINTS]\n {default,sensitivity} ...\n\n This building block uses MaBoSS to screen all the possible knockouts of a given Boolean model. It\n produces a candidate gene list formatted as a text file (single gene per row). More information on\n MaBoSS can be found in [Stoll G. et al. (2017)](https://academic.oup.com/bioinformatics/article-\n lookup/doi/10.1093/bioinformatics/btx123) and in the [MaBoSS GitHub\n repository](https://github.com/maboss-bkmc/MaBoSS-env-2.0).\n\n positional arguments:\n {default,sensitivity}\n\n options:\n -h, --help show this help message and exit\n -c CONFIG, --config CONFIG\n (CONFIG) Configuration file path\n -d, --debug Enable Building Block debug mode. Overrides log_level\n -l {debug,info,warning,error,critical}, --log_level {debug,info,warning,error,critical}\n Set logging level\n --tmpdir TMPDIR Temp directory to be mounted in the container\n --processes PROCESSES\n Number of processes for MPI executions\n --gpus GPUS Requirements for GPU jobs\n --memory MEMORY Memory requirement\n --mount_points MOUNT_POINTS\n Comma separated alias:folder to be mounted in the container\n\n ```\n\n - In particular for building blocks:\n\n ```shell\n $ permedcoe execute application -h\n usage: permedcoe execute application [-h] [-w {none,pycompss,nextflow,snakemake}]\n [-f FLAGS [FLAGS ...]]\n name [parameters [parameters ...]]\n\n positional arguments:\n name Application to execute\n parameters Application parameters (default: None)\n\n optional arguments:\n -h, --help show this help message and exit\n -w {none,pycompss,nextflow,snakemake}, --workflow_manager {none,pycompss,nextflow,snakemake}\n Workflow manager to use (default: none)\n -f FLAGS [FLAGS ...], --flags FLAGS [FLAGS ...]\n Workflow manager flags (default: None)\n ```\n\n#### Option template:\n\n- It available to create a skeleton of a building block or an application:\n\n ```shell\n $ permedcoe template -h\n usage: permedcoe template [-h] [-t {all,pycompss,nextflow,snakemake}]\n {bb,building_block,app,application} name\n\n positional arguments:\n {bb,building_block,app,application}\n Creates a Building Block or Application template.\n name Building Block or Application name.\n\n optional arguments:\n -h, --help show this help message and exit\n -t {all,pycompss,nextflow,snakemake}, --type {all,pycompss,nextflow,snakemake}\n Application type. (default: all)\n ```\n\n#### Option deploy:\n\n- It available to deploy an existing Building Block or Workflow in a **local machine (e.g. laptop)**:\n\n ```shell\n $ permedcoe deploy -h\n usage: permedcoe deploy [-h] {building_block,bb,workflow,wf} ...\n\n positional arguments:\n {building_block,bb,workflow,wf}\n building_block (bb)\n A specific building block.\n workflow (wf) A specific workflow.\n\n options:\n -h, --help show this help message and exit\n ```\n\nFor the deployment in supercomputers, please contact PerMedCoE: <https://permedcoe.eu/contact/>.\n\n### Public API\n\nThe `permedcoe` package provides a set of public decorators, parameter type definition and functions to be used in the Building Block implementation.\n\n- Public decorators:\n\n ```python\n from permedcoe import container\n from permedcoe import constraint\n from permedcoe import binary\n from permedcoe import mpi\n from permedcoe import task\n ```\n\n- Parameter type definition:\n\n ```python\n from permedcoe import Type\n from permedcoe import FILE_IN\n from permedcoe import FILE_OUT\n from permedcoe import FILE_INOUT\n from permedcoe import DIRECTORY_IN\n from permedcoe import DIRECTORY_OUT\n from permedcoe import DIRECTORY_INOUT\n from permedcoe import StdIOStream\n from permedcoe import STDIN\n from permedcoe import STDOUT\n from permedcoe import STDERR\n ```\n\n- Functions:\n\n ```python\n from permedcoe import get_environment\n from permedcoe import set_debug\n from permedcoe import invoker\n ```\n\n- Classes:\n\n ```python\n from permedcoe import Arguments\n ```\n\n### Uninstall\n\nUninstall can be done as usual `pip` packages:\n\nThere are two ways to uninstall this package, that depends on the way that it was installed (from Pypi or using `install.sh`):\n\n\n- From Pypi:\n\n ```shell\n pip uninstall permedcoe\n ```\n\n or more specifically:\n\n ```shell\n python3 -m pip uninstall permedcoe\n ```\n\n- From manual installation (using `install.sh`):\n\n ```shell\n ./uninstall.sh\n ```\n\n And then the folder can be cleaned as well using the `clean.sh` script.\n\n ```shell\n ./clean.sh\n ```\n\n## Developer instructions\n\n### Building block\n\nIf you are willing to implement your Building Block (BB), check the following repositories,\nwhere you will find documentation, tutorials, and BB/application samples:\n\n- [Documentation](https://permedcoe.readthedocs.io/en/latest/)\n- [Tutorial](https://permedcoe.readthedocs.io/en/latest/04_creating/04_tutorial/tutorial.html)\n- [basic_application](https://github.com/PerMedCoE/basic_application)\n- [Lysozyme_in_water](https://github.com/PerMedCoE/Lysozyme_in_water)\n\n## License\n\n[Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0)\n\n## Contact\n\n<https://permedcoe.eu/contact/>\n\nThis software has been developed for the [PerMedCoE project](https://permedcoe.eu/), funded by the European Commission (EU H2020 [951773](https://cordis.europa.eu/project/id/951773)).\n\n![](https://permedcoe.eu/wp-content/uploads/2020/11/logo_1.png \"PerMedCoE\")\n\n\n",
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