diff options
| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | doc/GUIX-Reproducible-from-source.org | 1 | ||||
| -rw-r--r-- | doc/README.org | 145 | ||||
| -rw-r--r-- | etc/default_settings.py | 3 |
4 files changed, 62 insertions, 89 deletions
@@ -4,6 +4,8 @@ *.bak *.cross *~ +*.swo +*.swp genotype_files/genotype/HSNIH_copy.geno web/new_genotypes/HSNIH.json wqflask/secure_server.py 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 620c946c..828ed2cd 100644 --- a/doc/README.org +++ b/doc/README.org @@ -3,17 +3,12 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - [[#install][Install]] - - [[#tarball][Tarball]] - - [[#docker][Docker]] - - [[#with-source][With source]] - [[#running-gn2][Running GN2]] - - [[#run-mysql-server][Run MySQL server]] - - [[#install-mysql-with-gnu-guix][Install MySQL with GNU GUIx]] + - [[#run-mariadb-server][Run MariaDB server]] + - [[#install-mariadb-with-gnu-guix][Install MariaDB with GNU GUIx]] - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] - - [[#running-elasticsearch][Running ElasticSearch]] - - [[#systemd][SystemD]] - [[#read-more][Read more]] - [[#trouble-shooting][Trouble shooting]] - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]] @@ -22,6 +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 @@ -40,44 +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 @@ -94,39 +57,48 @@ or you can set environment variables to override individual parameters, e.g. the debug and logging switches can be particularly useful when developing GN2. -* Run MySQL server -** Install MySQL with GNU GUIx +* Run MariaDB server +** Install MariaDB with GNU GUIx + +/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 #+BEGIN_SRC bash -adduser mysql && addgroup mysql -mysqld --datadir=/var/mysql --initialize-insecure -mkdir -p /var/run/mysqld -chown mysql.mysql ~/mysql /var/run/mysqld -mysqld -u mysql --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048" +adduser mariadb && addgroup mariadb +mysqld --datadir=/home/mariadb/database --initialize-insecure +mkdir -p /var/run/mariadbd +chown mariadb.mariadb /var/run/mariadbd +mysqld -u mariadb --datadir=/home/mariadb/database/mariadb --explicit_defaults_for_timestamp -P 12048" #+END_SRC If you want to run as root you may have to set : /etc/my.cnf -: [mysqld] +: [mariadbd] : user=root +You also need to set + +: ft_min_word_len = 3 + +To make sure word text searches (shh) work and rebuild the tables if +required. + To check error output in a file on start-up run with something like -: mysqld -u mysql --console --explicit_defaults_for_timestamp --datadir=/gnu/mysql --log-error=~/test.log +: mariadbd -u mariadb --console --explicit_defaults_for_timestamp --datadir=/gnu/mariadb --log-error=~/test.log -Other tips are that Guix installs mysqld in your profile, so this may work +Other tips are that Guix installs mariadbd in your profile, so this may work -: /home/user/.guix-profile/bin/mysqld -u mysql --explicit_defaults_for_timestamp --datadir=/gnu/mysql +: /home/user/.guix-profile/bin/mariadbd -u mariadb --explicit_defaults_for_timestamp --datadir=/gnu/mariadb When you get errors like: -: qlalchemy.exc.IntegrityError: (_mysql_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint') +: qlalchemy.exc.IntegrityError: (_mariadb_exceptions.IntegrityError) (1215, 'Cannot add foreign key constraint') you may need to set @@ -196,35 +168,6 @@ http://biogems.info/contrib/genenetwork/gn2.svg See [[development.org]]. -* Running ElasticSearch - -In order to start up elasticsearch: -Penguin - change user to "elasticsearch" and use the following command: "env JAVA_HOME=/opt/jdk-9.0.4 /opt/elasticsearch-6.2.1/bin/elasticsearch" - - -** SystemD - -New server - as root run "systemctl restart elasticsearch" - -#+BEGIN_SRC -tux01:/etc/systemd/system# cat elasticsearch.service -[Unit] -Description=Run Elasticsearch - -[Service] -ExecStart=/opt/elasticsearch-6.2.1/bin/elasticsearch -Environment=JAVA_HOME=/opt/jdk-9.0.4 -Environment="ES_JAVA_OPTS=-Xms1g -Xmx8g" -Environment="PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/jdk-9.0.4/bin" -LimitNOFILE=65536 -StandardOutput=syslog -StandardError=syslog -User=elasticsearch - -[Install] -WantedBy=multi-user.target -#+END_SRC - * Read more If you want to understand the architecture of GN2 read @@ -708,3 +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 diff --git a/etc/default_settings.py b/etc/default_settings.py index e01e4439..55f06a68 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -28,7 +28,8 @@ GN_VERSION = open("../etc/VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQL_ALCHEMY_POOL_RECYCLE = 3600 GN_SERVER_URL = "http://localhost:8880/" # REST API server -GN2_BASE_URL = "http://genenetwork.org/" # Main GN2 URL +GN2_BASE_URL = "http://genenetwork.org/" +GN2_BRANCH_URL = GN2_BASE_URL # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True |