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GeneNetwork version 1

Please see https://github.com/genenetwork for the most recent developments on GeneNetwork on GitHub.

Service initiated January, 1994 as The Portable Dictionary of the Mouse Genome and June 15, 2001 as WebQTL.

Funded by the National Institutes of Health and University of Tennessee Center for Integrative and Translational Genomics

For background see: http://en.wikipedia.org/wiki/Genenetwork

===========

Database

Genotypes

A number of directories contain data that are not checked into git. See this.

Production

For production

gn1@tux01:~/production/gnshare/gn$ . .guix-deploy

Note the extra dot. Copy and paste the URL in the container:

httpd -f /gnu/store/2g36jjrkn39d0npfrrl1rd7z0s8dp52s-httpd.conf

Zach

zas1024@tux01:~/gn1-zach/gnshare/gn$ . .guix-deploy

and paste

httpd -f /export/local/home/zas1024/gn1-zach/gnshare/gn/etc/httpd-zas1024.conf

Other

Running Genenetwork1 in modern environments can be difficult since its dependencies are no longer actively supported. With guix, however, we can reproduce the environment in which it ran. This is possible since some of the old (deprecated) packages are maintained in guix-past and guix-bioinformatics.

To host genenetwork1 in a guix container, run something like

#!/bin/sh

# Modify paths accordingly; or if you have your channels configured
# appropriately, you don't need to include the "-L" flags

/path/to/pre-inst-env guix environment \
    -L /path/to/guix-past/modules/ \
    -L /path/to/guix-bioinformatics/ \
    --pure \
    genenetwork1 \
    --ad-hoc \
    httpd-with-mod-python \
    python2@2.4 \
    python24-htmlgen-GN1 \
    python24-json-GN1 \
    python24-mysqlclient \
    python24-numarray \
    python24-piddle \
    python24-pp-GN1 \
    python24-pyx \
    python24-pyxlwriter \
    python24-qtlreaper \
    python24-rpy2 \
    python24-svg-GN1 \
    -- \
    httpd \
    -f \
    $(/path/to/pre-inst-env guix build -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ -e '(@ (gn services gn1-httpd-config) GN1-httpd-config)') \
    -T

This runs genenetwork1 on port 8042. To change the default port, modify: GN1-httpd-config in gn1-httpd-config.scm. Other default params you can modify are:

  • pid-file (default: "/tmp/guix-gn1/httpd-genenetwork1.pid")
  • error-log (default: "/tmp/guix-gn1/httpd-genenetwork1-error-log")

Ensure the above files exist and your user can write to those directories(i.e. /tmp/guix-gn1).

LICENSE

Released under Affero General Public License 3 (AGPLv3)