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| -rw-r--r-- | doc/GUIX-Reproducible-from-source.org | 1 | ||||
| -rw-r--r-- | doc/README.org | 80 |
2 files changed, 36 insertions, 45 deletions
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 83adce99..19e4d14f 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -33,7 +33,6 @@ GNU Guix has to be installed as root. I tested this recipe on a fresh install of Debian 8.3.0 (in KVM) though it should work on any modern Linux distribution (including CentOS). - Note that GN2 consists of an approx. 5 GB installation including database. If you use a virtual machine we recommend to use at least double. diff --git a/doc/README.org b/doc/README.org index 4057cb79..828ed2cd 100644 --- a/doc/README.org +++ b/doc/README.org @@ -3,9 +3,6 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - [[#install][Install]] - - [[#tarball][Tarball]] - - [[#docker][Docker]] - - [[#with-source][With source]] - [[#running-gn2][Running GN2]] - [[#run-mariadb-server][Run MariaDB server]] - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]] @@ -20,6 +17,8 @@ - [[#rpy2-error-show-now-found][Rpy2 error 'show' now found]] - [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]] - [[#irc-session][IRC session]] + - [[#notes][NOTES]] + - [[#deploying-gn2-official][Deploying GN2 official]] * Introduction @@ -38,44 +37,10 @@ an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]]. * Install -The quickest way to install GN2 is by using a binary installation -(tarball or Docker image). These installations are bundled by GNU -Guix and include all dependencies. You can install GeneNetwork on most -Linux distributions, including Debian, Ubuntu, Fedora and CentOS, -provided you have administrator privileges (root). The alternative is -a Docker installation. - -** Tarball - -Download the ~800Mb tarball from -[[http://files.genenetwork.org/software/binary_tarball/]]. Validate the checksum and -unpack to root, for example - -: tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz -: mv /gnu / -: mv /opt/genenetwork2 /opt/ - -Now you shoud be able to start the server with - -: /opt/genenetwork2/bin/genenetwork2 - -When the server stops with a MySQL error [[#run-mysql-server][Run MySQL server]] -and set SQL_URI to point at it. For example: - -: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s - -See also [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]. - -** Docker - -Docker images are also available through -[[http://files.genenetwork.org/software/]]. Validate the checksum and run -with [[https://docs.docker.com/engine/reference/commandline/load/][Docker load]]. - -** With source - -For more elaborate installation instructions on deploying GeneNetwork from -source see [[#source-deployment][Source deployment]]. +Make sure to install GNU Guix using the binary download instructions +on the main website. Follow the instructions on +[[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note +the download amounts to several GBs of data. * Running GN2 @@ -95,10 +60,10 @@ developing GN2. * Run MariaDB server ** Install MariaDB with GNU GUIx -/Note we are moving to MariaDB/ +/Note: we moved to MariaDB/ These are the steps you can take to install a fresh installation of -mysql (which comes as part of the GNU Guix genenetwork2 install). +mariadb (which comes as part of the GNU Guix genenetwork2 install). As root configure and run @@ -203,7 +168,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg See [[development.org]]. - * Read more If you want to understand the architecture of GN2 read @@ -687,3 +651,31 @@ The following derivations would be built: <pjotrp> I am building it on guix.genenetwork.org right now [10:09] <user01> nice [10:10] #+end_src + +* NOTES + +** Deploying GN2 official + +Let's see how fast we can deploy a second copy of GN2. + +- [-] Base install + + [X] First install a Debian server with GNU Guix on board + + [X] Get Guix build going + - [X] Build the correct version of Guix + - [X] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics + - [X] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable + + [X] Create a gn2 user and home with space + + [X] Install redis (currently debian) + - [X] add to systemd + - [X] update redis.cnf + - [X] update database + + [X] Install mariadb (currently debian mariadb-server) + - [X] add to systemd + - [X] system stop mysql + - [X] update mysql.cnf + - [X] update database (see gn-services/services/mariadb.md) + - [X] check tables + + [ ] run gn2 (rust-qtlreaper not working) + + [X] update nginx + + [ ] install genenetwork3 + - [ ] add to systemd |