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R2915/example_pipelines/SIB-publications/README.md
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SIB Publications
================
Note: this is a snapshot of a simplified version used in SIB and stored in gitlab.sib.swiss
* Applications to obtain SIB publications registered in EuropePMC.org.
* SIB-monthly-publications.py - get specific year-month publications with affiliation 'Swiss Institute of Bioinformatics'
* Aim is to provide a web page source with all publications.
* Docker client is required - Singularity is optional
Usage:
------
# copy the project locally
# Docker
## MAC Users - make sure Docker client is not running
```
docker rm $(docker ps -a -q)
docker rmi $(docker images -q)
docker volume rm $(docker volume ls |awk '{print $2}')
rm -rf ~/Library/Containers/com.docker.docker/Data/*
```
### create docker image - CentOS 7, python 3.6 and the ICU library to sort unicode strings
```
cd SIB-publications
```
### start Docker client if necessary, then build the docker image (2-3 minutes)
docker build -t sib-publications .
### run the image - by default, all publications of the current year/previous month are retrieved
```
docker run -v $(pwd)/data:/data sib-publications /data/SIB-monthly-publications.py
docker run -v $(pwd)/data:/data sib-publications /data/SIB-monthly-publications.py 2016 4
```
Results - SIB-monthly-publications.py
--------
* List of all SIB publication IDs:
* `requestedYear_dateOfRun-all-SIB-IDs.txt`
* Html page for SIB communications:
* `requestedYear_dateOfRun-all-SIB-publications.txt`
# Singularity [optional]:
## Linux Users
### convert the docker image to a singularity compliant image
```
docker run -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):/output --privileged -t --rm singularityware/docker2singularity sib-publications
```
### run the image - by default, all publications of the current year/previous month are retrieved
```
singularity run -B ./data:/data sib-publications.img /data/SIB-monthly-publications.py
singularity run -B ./data:/data sib-publications.img /data/SIB-monthly-publications.py 2017 01
```
## MAC Users - install Singularity/Vagrant
### convert the docker image to a singularity compliant image
```
docker run -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):/output --privileged -t --rm singularityware/docker2singularity sib-publications
```
### mv all necessary files including the newly created singularity compliant image to vagrant directory
### optional - rename image filename
```
mv sib-publications-2017-06-25-c64d5ab14745.img sib-publications.img
```
### docroot is an additional directory to the standard Vagrant installation
```
mkdir ~/Desktop/scratch/singularity-vm/docroot
mv sib-publications.img ~/Desktop/scratch/singularity-vm/docroot/
# data directory contains
# the python script 'SIB-GL-publications.py'
# the conf directory containing the file 'list-of-GLs.csv'
cp -r data ~/Desktop/scratch/singularity-vm/docroot
cd ~/Desktop/scratch/singularity-vm/
```
### edit the Vagrantfile by adding the following line if necessary
### config.vm.synced_folder "docroot", "/data", :mount_options => ['dmode=775', 'fmode=664']
### start or reload vagrant virtual machine
```
vagrant reload
vagrant ssh
```
### from vagrant-console
```
cd /data
```
### run singularity
(same as Linux above)
Important:
----------
* Needs Docker to create the image and to run the container
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