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

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cbg-ethz/conda_stats_gather

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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 [email protected]: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

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

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