diff options
Diffstat (limited to 'topics/deploy')
| -rw-r--r-- | topics/deploy/installation.gmi | 118 |
1 files changed, 14 insertions, 104 deletions
diff --git a/topics/deploy/installation.gmi b/topics/deploy/installation.gmi index 53e0e0c..2e6a3b1 100644 --- a/topics/deploy/installation.gmi +++ b/topics/deploy/installation.gmi @@ -321,17 +321,17 @@ material. Download one database from -http://ipfs.genenetwork.org/ipfs/QmRUmYu6ogxEdzZeE8PuXMGCDa8M3y2uFcfo4zqQRbpxtk +=> https://files.genenetwork.org/database/ -After installation unzip the database binary in the MySQL directory +After installation unzip the database binary in the MySQL directory, e.g. -#+BEGIN_SRC sh +``` cd ~/mysql p7zip -d db_webqtl_s.7z chown -R mysql:mysql db_webqtl_s/ chmod 700 db_webqtl_s/ chmod 660 db_webqtl_s/* -#+END_SRC +``` restart MySQL service (mysqld). Login as root @@ -365,84 +365,22 @@ configuration (see below). Note for the plant database you can rename it to db_webqtl_s, or change the settings in etc/default_settings.py to match your path. -* Get genotype files - -The script looks for genotype files. You can find them in -http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL - -#+BEGIN_SRC sh -mkdir -p $HOME/genotype_files -cd $HOME/genotype_files - -#+END_SRC - -* GN2 Dependency Graph - -List of all runtime dependencies for GN2 as installed by GNU Guix. - -https://genenetwork.org/environments/ - -* Working with the GN2 source code - -See [[development.org]]. - -* Read more - -If you want to understand the architecture of GN2 read -[[Architecture.org]]. The rest of this document is mostly on deployment -of GN2. - -* Trouble shooting +# Get genotype files -** ImportError: No module named jinja2 +The script looks for genotype files. You can find a BXD subset in -If you have all the Guix packages installed this error points out that -the environment variables are not set. Copy-paste the paths into your -terminal (mainly so PYTHON_PATH and R_LIBS_SITE are set) from the -information given by guix: +=> https://files.genenetwork.org/genotype_files/ -: guix package --search-paths +(Note we should add plants) -On one system: - -: export PYTHONPATH="$HOME/.guix-profile/lib/python3.8/site-packages" -: export R_LIBS_SITE="$HOME/.guix-profile/site-library/" -: export GEM_PATH="$HOME/.guix-profile/lib/ruby/gems/2.2.0" - -and perhaps a few more. -** ERROR: 'can not find directory $HOME/gn2_data' or 'can not find directory $HOME/genotype_files/genotype' - -The default settings file looks in your $HOME/gn2_data. Since these -files come with a Guix installation you should take a hint from the -values in the installed version of default_settings.py (see above in -this document). - -You can use the GENENETWORK_FILES switch to set the datadir, for example - -: env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=/gnu/data/gn2_data ./bin/genenetwork2 - -** Can't run a module - -In rare cases, development modules are not brought in with Guix -because no source code is available. This can lead to missing modules -on a running server. Please check with the authors when a module -is missing. -** Rpy2 error 'show' now found - -This error - -: __show = rpy2.rinterface.baseenv.get("show") -: LookupError: 'show' not found - -means that R was updated in your path, and that Rpy2 needs to be -recompiled against this R - don't you love informative messages? +``` +mkdir -p $HOME/genotype_files +cd $HOME/genotype_files +``` -In our case it means that GN's PYTHONPATH is not in sync with -R_LIBS_SITE. Please check your GNU Guix GN2 installation paths, -you man need to reinstall. Note that this may be the point you -may want to start using profiles (see profile section). +# Trouble shooting -** Mysql can't connect server through socket ERROR +## Mysql can't connect server through socket ERROR The following error @@ -460,31 +398,3 @@ try to connect over the network interface instead, e.g. if that works run genenetwork after setting SQL_URI to something like : export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s - -* NOTES - -** Deploying GN2 official - -Let's see how fast we can deploy a second copy of GN2. - -- [ ] Base install - + [ ] First install a Debian server with GNU Guix on board - + [ ] Get Guix build going - - [ ] Build the correct version of Guix - - [ ] Check out the correct gn-stable version of guix-bioinformatics http://git.genenetwork.org/pjotrp/guix-bioinformatics - - [ ] guix package -i genenetwork2 -p /usr/local/guix-profiles/gn2-stable - + [ ] Create a gn2 user and home with space - + [ ] Install redis - - [ ] add to systemd - - [ ] update redis.cnf - - [ ] update database - + [ ] Install mariadb (currently debian mariadb-server) - - [ ] add to systemd - - [ ] system stop mysql - - [ ] update mysql.cnf - - [ ] update database (see gn-services/services/mariadb.md) - - [ ] check tables - + [ ] run gn2 - + [ ] update nginx - + [ ] install genenetwork3 - - [ ] add to systemd |