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Open Source Science

https://github.com/cbg-ethz/conda_stats_gather

Used to track downloads of bioconda packages used by V-pipe, see: https://cbg-ethz.github.io/V-pipe/pipeline/

https://github.com/cbg-ethz/conda_stats_gather

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Used to track downloads of bioconda packages used by V-pipe, see: https://cbg-ethz.github.io/V-pipe/pipeline/

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • Language: Perl
  • Default Branch: master
  • Size: 24.4 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Installing on RedHat 7

Inside ETHZ network, the server is accessible at :

production-server is the branch currently deployed on the server

sudo setfacl --modify='g:bsse-beerenwinkel:rwx' /opt
sudo git clone --shared --branch production-server git@github.com:DrYak/conda_stats_gather.git
cd conda_stats_gather

Dependencies

RH7 has out dated Perl and Python. Luckily SCL (software Collection) makes it possible to install more modern stacks

sudo yum install texlive-latex-bin-bin  texlive-pdfpages texlive-pdftex-def texlive-ifluatex texlive-collection-fontsrecommended
sudo yum install rh-perl526-perl
sudo yum install rh-python36 rh-python36-python-six rh-python36-numpy rh-python36-scipy rh-python36-python-pip rh-python36-python-setuptools
scl enable rh-python36 -- sudo pip3 install matplotlib pandas seaborn

wget -O- http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic/firth/software/pdfjam/pdfjam_latest.tgz | tar xzC /opt
sudo ln -sf /opt/pdfjam/bin/pdfjam /usr/local/bin/

scl enable rh-python36 -- scl enable rh-perl526 -- make

Installing services

sudo systemctl link /opt/conda_stats_gather/conda_stats_gather.service
sudo systemctl link /opt/conda_stats_gather/conda_stats_gather.timer
sudo systemctl link /opt/conda_stats_gather/make_pdf.service
sudo systemctl link /opt/conda_stats_gather/make_pdf.timer
sudo systemctl daemon-reload
sudo systemctl enable conda_stats_gather.service
sudo systemctl enable /opt/conda_stats_gather/conda_stats_gather.timer
sudo systemctl start conda_stats_gather.timer
sudo systemctl enable /opt/conda_stats_gather/make_pdf.timer
sudo systemctl start make_pdf.timer
systemctl list-timers -a

Webserver

Note there is a bug in the default RedHat lighttpd configuration. (As the logs will tell you: *use server.use-ipv6 only for hostnames, not without server.bind / empty address)

sudo yum install lighttpd
sudo sed -i -r s@^(server.use-ipv6.*)$@#\1@g';s@^#(include.*vhosts\.d.*)$@\1@g' /etc/lighttpd/lighttpd.conf
sudo ln -s /opt/conda_stats_gather/stats.lighttpd.conf /etc/lighttpd/vhosts.d/90-stats.conf
sudo systemctl restart lighttpd.service
sudo systemctl status lighttpd.service

Firewall

/etc/sysconfig/iptables needs the following extra rules :

-A RH-Firewall-1-INPUT -p tcp -m state --state NEW -m tcp --dport 80 -j ACCEPT
-A RH-Firewall-1-INPUT -p tcp -m state --state NEW -m tcp --dport 443 -j ACCEPT

Then:

sudo systemctl reload iptables.service
sudo /sbin/iptables -L

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

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Last synced: over 1 year ago

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  • Bot pull requests: 0
Past Year
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  • Pull requests: 0
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  • Average time to close pull requests: N/A
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  • Pull request authors: 0
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