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-rw-r--r--doc/GUIX-Reproducible-from-source.org1
-rw-r--r--doc/README.org80
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