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

1. Docker
   1. 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]:

1. Linux Users
   1. 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

1. MAC Users - install Singularity/Vagrant
   1. 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

1. mv all necessary files including the newly created singularity compliant image to vagrant directory
2. 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/

1. edit the Vagrantfile by adding the following line if necessary
2. 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