From 8677d1b7bd5b32791c440bf0de2fc4c61c98299f Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sun, 21 May 2017 07:21:44 +0000 Subject: Merge from the diet branch. * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile --- doc/GUIX-Reproducible-from-source.org | 356 ++++++++++++++++++++++++++- doc/README.org | 440 ++++++++-------------------------- doc/development.org | 23 ++ 3 files changed, 478 insertions(+), 341 deletions(-) create mode 100644 doc/development.org (limited to 'doc') diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org index 4399ea26..83adce99 100644 --- a/doc/GUIX-Reproducible-from-source.org +++ b/doc/GUIX-Reproducible-from-source.org @@ -2,19 +2,188 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - - [[#binary-deployment][Binary deployment]] + - [[#binary-deployment-through-gnu-guix][Binary deployment through GNU Guix]] + - [[#quick-installation-recipe][Quick installation recipe]] + - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]] + - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]] + - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]] + - [[#step-4-install-and-run-gn2][Step 4: Install and run GN2]] - [[#from-source-deployment][From source deployment]] - [[#create-archive][Create archive]] + - [[#source-deployment][Source deployment]] + - [[#run-your-own-copy-of-gn2][Run your own copy of GN2]] + - [[#set-up-nginx-port-forwarding][Set up nginx port forwarding]] + - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]] + - [[#update-to-recent-guix][Update to recent guix]] + - [[#install-gn2][Install GN2]] + - [[#run-gn2][Run GN2]] * Introduction Large system deployments tend to get very complex. In this document we explain the GeneNetwork deployment system which is based on GNU Guix -(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). +(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]] and the main [[README.org]] doc). -* Binary deployment +* Binary deployment through GNU Guix +** Quick installation recipe -NYA (will go to README) +This is a recipe for quick and dirty installation of GN2. For +convenience everything is installed as root, though in reality only +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. + +** Step 1: Install GNU Guix + +Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow +[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially, download and unpack the tar ball (which +creates directories in /gnu and /var/guix), add build users and group +(Guix builds software as unpriviliged users) and run the Guix daemon +after fixing the paths (also known as the 'profile'). + +Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission +to download binaries from the GNU server) and you should be able to +install the hello package using binary packages (no building) + +#+begin_src bash +export PATH=~/.guix-profile/bin:$PATH +guix pull +guix package -i hello --dry-run +#+end_src + +Which should show something like + +: The following files would be downloaded: +: /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10 +: ... +#+end_src + +means binary installs. The actual installation command of 'hello' is + +#+begin_src bash +guix package -i hello +hello + Hello, world! +#+end_src + +If you actually see things building it means that Guix is not yet +properly installed and up-to-date, i.e., the key is missing or you +need to do a 'guix pull'. Press Ctrl-C to interrupt. + +If you need more help we have another writeup in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation][guix-notes]]. To get +rid of the locale warning see [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale][set-locale]]. + +** Step 2: Checkout the GN2 git repositories + +To fixate the software dependency graph GN2 uses git repositories of +Guix packages. First install git if it is missing + +#+begin_src bash +guix package -i git +export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt +#+end_src + +check out the git repositories (gn-deploy branch) + +#+begin_src bash +cd ~ +mkdir genenetwork +cd genenetwork +git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics +git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy +cd guix-gn-deploy +#+end_src bash + +To test whether this is working try: + +#+begin_src bash +#+end_src bash + +** Step 3: Authorize the GN Guix server + +GN2 has its own GNU Guix binary distribution server. To trust it you have +to add the following key + +#+begin_src scheme +(public-key + (ecc + (curve Ed25519) + (q #11217788B41ADC8D5B8E71BD87EF699C65312EC387752899FE9C888856F5C769#) + ) +) +#+end_src + +by pasting it into the command + +#+begin_src bash +guix archive --authorize +#+end_src + +and hit Ctrl-D. + +Now you can use the substitute server to install GN2 binaries. + +** Step 4: Install and run GN2 + +Since this is a quick and dirty install we are going to override the +GNU Guix package path by pointing the package path to our repository: + +#+begin_src bash +rm /root/.config/guix/latest +ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest +#+end_src + +Now check whether you can find the GN2 package with + +#+begin_src bash +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2 + genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2 +#+end_src + +(ignore the source file newer then ... messages, this is caused by the +/root/.config/guix/latest override). + +And install with + +#+begin_src bash +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \ + guix package -i genenetwork2 \ + --substitute-urls="http://guix.genenetwork.org" +#+end_src + +Note: the order of the substitute url's may make a difference in speed +(put the one first that is fastest for your location and time of day). + +Note: if your system starts building or gives an error it may well be +Step 3 did not succeed. The installation should actually be smooth at +this point and only do binary installs (no compiling). + +After installation you should be able to run genenetwork2 after updating +the Guix suggested environment vars. Check the output of + +#+begin_src bash +guix package --search-paths +export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages" +export R_LIBS_SITE="/root/.guix-profile/site-library/" +#+end_src + +and copy-paste the listed exports into the terminal before running: + +#+begin_src bash +genenetwork2 +#+end_src + +It will complain that the database is missing. See the next section on +running MySQL server for downloading and installing a MySQL GN2 +database. After installing the database restart genenetwork2 and point +your browser at [[http://localhost:5003/]]. + +End of the GN2 installation recipe! * From source deployment @@ -52,3 +221,182 @@ gn-stable-guix$ env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix * Create archive : env GUIX_PACKAGE_PATH=../../genenetwork/guix-bioinformatics/ ./pre-inst-env guix archive --export -r genenetwork2 > guix_gn2-2.0-9e9475053.nar + + +* Source deployment + +This section gives a more elaborate instruction for installing GN2 +from source. + +First execute above 4 steps: + + - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]] + - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]] + - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]] + - [[#step-4-install-and-run-gn2-][Step 4: Install and run GN2 ]] + + +** Run your own copy of GN2 + +At some point you may want to fix the source code. Assuming you have +Guix and Genenetwork2 installed (as described above) clone the GN2 +repository from https://github.com/genenetwork/genenetwork2. + +Copy-paste the paths into your terminal (mainly so PYTHON_PATH and +R_LIBS_SITE are set) from the information given by guix: + +: guix package --search-paths + +Inside the repository: + +: cd genenetwork2 +: ./bin/genenetwork2 + +Will fire up your local repo http://localhost:5003/ using the +settings in ./etc/default_settings.py. These settings may +not reflect your system. To override settings create your own from a copy of +default_settings.py and pass it into GN2 with + +: ./bin/genenetwork2 $HOME/my_settings.py + +and everything *should* work (note the full path to the settings +file). This way we develop against the exact same dependency graph of +software. + +If something is not working, take a hint from the settings file +that comes in the Guix installation. It sits in something like + +: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py + +** Set up nginx port forwarding + +nginx can be used as a reverse proxy for GN2. For example, we want to +expose GN2 on port 80 while it is running on port 5003. Essentially +the configuration looks like + +#+begin_src js + server { + listen 80; + server_name test-gn2.genenetwork.org; + access_log logs/test-gn2.access.log; + + proxy_connect_timeout 3000; + proxy_send_timeout 3000; + proxy_read_timeout 3000; + send_timeout 3000; + + location / { + proxy_set_header Host $http_host; + proxy_set_header Connection keep-alive; + proxy_set_header X-Real-IP $remote_addr; + proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; + proxy_set_header X-Forwarded-Host $server_name; + proxy_pass http://127.0.0.1:5003; + } +} +#+end_src js + +Install the nginx webserver (as root) + +: guix package -i nginx + +The nginx example configuration examples can be found in the Guix +store through + +: ls -l /root/.guix-profile/sbin/nginx +: lrwxrwxrwx 3 root guixbuild 66 Dec 31 1969 /root/.guix-profile/sbin/nginx -> /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/sbin/nginx + +Use that path + +: ls /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/share/nginx/conf/ +: fastcgi.conf koi-win scgi_params +: fastcgi.conf.default mime.types scgi_params.default +: fastcgi_params mime.types.default uwsgi_params +: fastcgi_params.default nginx.conf uwsgi_params.default +: koi-utf nginx.conf.default win-utf + +And copy any relevant files to /etc/nginx. A configuration file for +GeneNetwork (reverse proxy) port forwarding can be found in the source +repository under ./etc/nginx-genenetwork.conf. Copy this file to /etc +(still as root) +: cp ./etc/nginx-genenetwork.conf /etc/nginx/ + +Make dirs + +: mkdir -p /var/spool/nginx/logs + +Add users + +: adduser nobody ; addgroup nobody + +Run nginx + +: /root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx + +* Source deployment and other information on reproducibility + +See the document [[GUIX-Reproducible-from-source.org]]. + +** Update to recent guix + +We now compile Guix from scratch. + +Create, install and run a recent version of the guix-daemon by +compiling the guix repository you have installed with git in +step 2. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully after + +: cd ~/genenetwork/guix-gn-deploy + +Make sure to restart the guix daemon and run guix client from this +directory. + +** Install GN2 + +Reinstall genenetwork2 using the new tree + +#+begin_src bash +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org" +#+end_src bash + +Note the use of ./pre-inst-env here! + +Actually, it should be the same installation as in step 4, so nothing +gets downloaded. + +** Run GN2 + +Make a note of the paths with + +#+begin_src bash +./pre-inst-env guix package --search-paths +#+end_src bash + +or this should also work if guix is installed + +#+begin_src bash +guix package --search-paths +#+end_src bash + +After setting the paths for the server + +#+begin_src bash +export PATH=~/.guix-profile/bin:$PATH +export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" +export R_LIBS_SITE="$HOME/.guix-profile/site-library/" +export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0" +export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0" +export XDG_DATA_DIRS="$HOME/.guix-profile/share" +export GIO_EXTRA_MODULES="$HOME/.guix-profile/lib/gio/modules" +#+end_src bash + +run the main script (in ~/.guix-profile/bin) + +#+begin_src bash +genenetwork2 +#+end_src bash + +will start the default server which listens on port 5003, i.e., +http://localhost:5003/. + +OK, we are where we were before with step 4. Only difference is that we +used our own compiled guix server. diff --git a/doc/README.org b/doc/README.org index b38ea664..a39ef603 100644 --- a/doc/README.org +++ b/doc/README.org @@ -2,33 +2,27 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - - [[#quick-installation-recipe][Quick installation recipe]] - - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]] - - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]] - - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]] - - [[#step-4-install-and-run-gn2][Step 4: Install and run GN2]] + - [[#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]] + - [[#load-the-small-database-in-mysql][Load the small database in MySQL]] - [[#gn2-dependency-graph][GN2 Dependency Graph]] - - [[#source-deployment][Source deployment]] - - [[#run-your-own-copy-of-gn2][Run your own copy of GN2]] - - [[#set-up-nginx-port-forwarding][Set up nginx port forwarding]] - - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]] - - [[#update-to-recent-guix][Update to recent guix]] - - [[#install-gn2][Install GN2]] - - [[#run-gn2][Run GN2]] + - [[#working-with-the-gn2-source-code][Working with the GN2 source code]] - [[#trouble-shooting][Trouble shooting]] - [[#importerror-no-module-named-jinja2][ImportError: No module named jinja2]] - [[#error-can-not-find-directory-homegn2_data][ERROR: can not find directory $HOME/gn2_data]] - [[#cant-run-a-module][Can't run a module]] - [[#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]] + - [[#read-more][Read more]] - [[#irc-session][IRC session]] * Introduction -If you want to understand the architecture of GN2 read -[[Architecture.org]]. The rest of this document is mostly on deployment -of GN2. - Large system deployments can get very [[http://biogems.info/contrib/genenetwork/gn2.svg ][complex]]. In this document we explain the GeneNetwork version 2 (GN2) reproducible deployment system which is based on GNU Guix (see also [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix @@ -37,195 +31,113 @@ system can be used to install GN with all its files and dependencies. The official installation path is from a checked out version of the main Guix package tree and that of the Genenetwork package tree. Current supported versions can be found as the SHA values of -'gn-latest' branches of [[https://github.com/genenetwork/guix-bioinformatics/tree/gn-latest][Guix bioinformatics]] and [[https://github.com/genenetwork/guix/tree/gn-latest][GNU Guix main]]. +'gn-latest' branches of [[https://gitlab.com/genenetwork/guix-bioinformatics][Guix bioinformatics]] and [[https://gitlab.com/genenetwork/guix][GNU Guix]]. For a full view of runtime dependencies as defined by GNU Guix, see -the [[#gn2-dependency-graph][GN2 Dependency Graph]]. - -* Quick installation recipe - -This is a recipe for quick and dirty installation of GN2. For -convenience everything is installed as root, though in reality only -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). For more elaborate installation -instructions see [[#source-deployment][Source deployment]]. - -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. - -** Step 1: Install GNU Guix - -Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow -[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially, download and unpack the tar ball (which -creates directories in /gnu and /var/guix), add build users and group -(Guix builds software as unpriviliged users) and run the Guix daemon -after fixing the paths (also known as the 'profile'). - -Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission -to download binaries from the GNU server) and you should be able to -install the hello package using binary packages (no building) - -#+begin_src bash -export PATH=~/.guix-profile/bin:$PATH -guix pull -guix package -i hello --dry-run -#+end_src - -Which should show something like - -: The following files would be downloaded: -: /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10 -: ... -#+end_src - -means binary installs. The actual installation command of 'hello' is - -#+begin_src bash -guix package -i hello -hello - Hello, world! -#+end_src - -If you actually see things building it means that Guix is not yet -properly installed and up-to-date, i.e., the key is missing or you -need to do a 'guix pull'. Press Ctrl-C to interrupt. - -If you need more help we have another writeup in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation][guix-notes]]. To get -rid of the locale warning see [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale][set-locale]]. - -** Step 2: Checkout the GN2 git repositories +an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]]. -To fixate the software dependency graph GN2 uses git repositories of -Guix packages. First install git if it is missing +* Install -#+begin_src bash -guix package -i git -export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt -#+end_src +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. -check out the git repositories (gn-deploy branch) +** Tarball -#+begin_src bash -cd ~ -mkdir genenetwork -cd genenetwork -git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics -git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy -cd guix-gn-deploy -#+end_src bash +Download the ~800Mb tarball from +[[http://files.genenetwork.org/software/binary_tarball/]]. Validate the checksum and +unpack to root, for example -To test whether this is working try: +: tar xvzf genenetwork2-2.10rc3-1538ffd-tarball-pack.tar.gz +: mv /gnu / +: mv /opt/genenetwork2 /opt/ -#+begin_src bash -#+end_src bash +Now you shoud be able to start the server with +: /opt/genenetwork2/bin/genenetwork2 -** Step 3: Authorize the GN Guix server +When the server stops with a MySQL error [[#run-mysql-server][Run MySQL server]] +and set SQL_URI to point at it. For example: -GN2 has its own GNU Guix binary distribution server. To trust it you have -to add the following key +: export SQL_URI=mysql://gn2:mysql_password@127.0.0.1/db_webqtl_s -#+begin_src scheme -(public-key - (ecc - (curve Ed25519) - (q #11217788B41ADC8D5B8E71BD87EF699C65312EC387752899FE9C888856F5C769#) - ) -) -#+end_src +See also [[#mysql-cant-connect-server-through-socket-error][Mysql can't connect server through socket ERROR]]. -by pasting it into the command +** Docker -#+begin_src bash -guix archive --authorize -#+end_src +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]]. -and hit Ctrl-D. +** With source -Now you can use the substitute server to install GN2 binaries. +For more elaborate installation instructions on deploying GeneNetwork from +source see [[#source-deployment][Source deployment]]. -** Step 4: Install and run GN2 +* Running GN2 -Since this is a quick and dirty install we are going to override the -GNU Guix package path by pointing the package path to our repository: +Default settings for GN2 are listed in a file called +[[../etc/default_settings.py][default_settings.py]]. You can copy this file and pass it as a new +parameter to the genenetwork2 command, e.g. -#+begin_src bash -rm /root/.config/guix/latest -ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest -#+end_src +: genenetwork2 mysettings.py -Now check whether you can find the GN2 package with +or you can set environment variables to override individual parameters, e.g. -#+begin_src bash -env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2 - genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2 -#+end_src - -(ignore the source file newer then ... messages, this is caused by the -/root/.config/guix/latest override). +: env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2 -And install with +the debug and logging switches can be particularly useful when +developing GN2. -#+begin_src bash -env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \ - guix package -i genenetwork2 \ - --substitute-urls="http://guix.genenetwork.org" -#+end_src - -Note: the order of the substitute url's may make a difference in speed -(put the one first that is fastest for your location and time of day). - -Note: if your system starts building or gives an error it may well be -Step 3 did not succeed. The installation should actually be smooth at -this point and only do binary installs (no compiling). - -After installation you should be able to run genenetwork2 after updating -the Guix suggested environment vars. Check the output of - -#+begin_src bash -guix package --search-paths -export PYTHONPATH="/root/.guix-profile/lib/python2.7/site-packages" -export R_LIBS_SITE="/root/.guix-profile/site-library/" -#+end_src +* Run MySQL server +** Install MySQL with GNU GUIx -and copy-paste the listed exports into the terminal before running: +These are the steps you can take to install a fresh installation of +mysql (which comes as part of the GNU Guix genenetwork2 install). -#+begin_src bash -genenetwork2 -#+end_src +As root configure and run -It will complain that the database is missing. See the next section on -running MySQL server for downloading and installing a MySQL GN2 -database. After installing the database restart genenetwork2 and point -your browser at [[http://localhost:5003/]]. +: adduser mysql && addgroup mysql +: mysqld --datadir=/var/mysql --initialize-insecure +: mkdir -p /var/run/mysqld +: chown mysql.mysql ~/mysql /var/run/mysqld +: su mysql -c mysqld --datadir=/var/mysql --explicit_defaults_for_timestamp -P 12048 -End of the GN2 installation recipe! +/etc/my.cnf +[mysqld] +user=root -* Run MySQL server +** Load the small database in MySQL At this point we require the underlying distribution to install and -run mysqld. Currently we have two databases for deployment, +run mysqld (see next section for GNU Guix). Currently we have two databases for deployment, 'db_webqtl_s' is the small testing database containing experiments from BXD mice and 'db_webqtl_plant' which contains all plant related material. Download one database from -http://files.genenetwork.org/raw_database/ -https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip +[[http://files.genenetwork.org/raw_database/]] + +[[https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip]] Check the md5sum. After installation inflate the database binary in the MySQL directory -(this installation path is subject to change soon) +: cd ~/mysql : chown -R mysql:mysql db_webqtl_s/ : chmod 700 db_webqtl_s/ : chmod 660 db_webqtl_s/* -restart MySQL service (mysqld). Login as root and +restart MySQL service (mysqld). Login as root + +: myslq -u root + +and : mysql> show databases; : +--------------------+ @@ -241,9 +153,12 @@ Set permissions and match password in your settings file below: : mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password'; +You may need to change "localhost" to whatever domain you are +connecting from (mysql will give an error). + Note that if the mysql connection is not working, try connecting to the IP address and check server firewall, hosts.allow and mysql IP -configuration. +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. @@ -255,183 +170,9 @@ Graph of all runtime dependencies as installed by GNU Guix. #+ATTR_HTML: :title GN2_graph http://biogems.info/contrib/genenetwork/gn2.svg -* Source deployment - -This section gives a more elaborate instruction for installing GN2 -from source. - -First execute above 4 steps: - - - [[#step-1-install-gnu-guix][Step 1: Install GNU Guix]] - - [[#step-2-checkout-the-gn2-git-repositories][Step 2: Checkout the GN2 git repositories]] - - [[#step-3-authorize-the-gn-guix-server][Step 3: Authorize the GN Guix server]] - - [[#step-4-install-and-run-gn2-][Step 4: Install and run GN2 ]] - - -** Run your own copy of GN2 - -At some point you may want to fix the source code. Assuming you have -Guix and Genenetwork2 installed (as described above) clone the GN2 -repository from https://github.com/genenetwork/genenetwork2. - -Copy-paste the paths into your terminal (mainly so PYTHON_PATH and -R_LIBS_SITE are set) from the information given by guix: - -: guix package --search-paths - -Inside the repository: - -: cd genenetwork2 -: ./bin/genenetwork2 - -Will fire up your local repo http://localhost:5003/ using the -settings in ./etc/default_settings.py. These settings may -not reflect your system. To override settings create your own from a copy of -default_settings.py and pass it into GN2 with - -: ./bin/genenetwork2 $HOME/my_settings.py - -and everything *should* work (note the full path to the settings -file). This way we develop against the exact same dependency graph of -software. - -If something is not working, take a hint from the settings file -that comes in the Guix installation. It sits in something like +* Working with the GN2 source code -: cat ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py - -** Set up nginx port forwarding - -nginx can be used as a reverse proxy for GN2. For example, we want to -expose GN2 on port 80 while it is running on port 5003. Essentially -the configuration looks like - -#+begin_src js - server { - listen 80; - server_name test-gn2.genenetwork.org; - access_log logs/test-gn2.access.log; - - proxy_connect_timeout 3000; - proxy_send_timeout 3000; - proxy_read_timeout 3000; - send_timeout 3000; - - location / { - proxy_set_header Host $http_host; - proxy_set_header Connection keep-alive; - proxy_set_header X-Real-IP $remote_addr; - proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; - proxy_set_header X-Forwarded-Host $server_name; - proxy_pass http://127.0.0.1:5003; - } -} -#+end_src js - -Install the nginx webserver (as root) - -: guix package -i nginx - -The nginx example configuration examples can be found in the Guix -store through - -: ls -l /root/.guix-profile/sbin/nginx -: lrwxrwxrwx 3 root guixbuild 66 Dec 31 1969 /root/.guix-profile/sbin/nginx -> /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/sbin/nginx - -Use that path - -: ls /gnu/store/g0wrcl5z27rmk5b52rldzvk1bzzbnz2l-nginx-1.8.1/share/nginx/conf/ -: fastcgi.conf koi-win scgi_params -: fastcgi.conf.default mime.types scgi_params.default -: fastcgi_params mime.types.default uwsgi_params -: fastcgi_params.default nginx.conf uwsgi_params.default -: koi-utf nginx.conf.default win-utf - -And copy any relevant files to /etc/nginx. A configuration file for -GeneNetwork (reverse proxy) port forwarding can be found in the source -repository under ./etc/nginx-genenetwork.conf. Copy this file to /etc -(still as root) -: cp ./etc/nginx-genenetwork.conf /etc/nginx/ - -Make dirs - -: mkdir -p /var/spool/nginx/logs - -Add users - -: adduser nobody ; addgroup nobody - -Run nginx - -: /root/.guix-profile/sbin/nginx -c /etc/nginx/nginx-genenetwork.conf -p /var/spool/nginx - -* Source deployment and other information on reproducibility - -See the document [[GUIX-Reproducible-from-source.org]]. - -** Update to recent guix - -We now compile Guix from scratch. - -Create, install and run a recent version of the guix-daemon by -compiling the guix repository you have installed with git in -step 2. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully after - -: cd ~/genenetwork/guix-gn-deploy - -Make sure to restart the guix daemon and run guix client from this -directory. - -** Install GN2 - -Reinstall genenetwork2 using the new tree - -#+begin_src bash -env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org" -#+end_src bash - -Note the use of ./pre-inst-env here! - -Actually, it should be the same installation as in step 4, so nothing -gets downloaded. - -** Run GN2 - -Make a note of the paths with - -#+begin_src bash -./pre-inst-env guix package --search-paths -#+end_src bash - -or this should also work if guix is installed - -#+begin_src bash -guix package --search-paths -#+end_src bash - -After setting the paths for the server - -#+begin_src bash -export PATH=~/.guix-profile/bin:$PATH -export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" -export R_LIBS_SITE="$HOME/.guix-profile/site-library/" -export GUIX_GTK3_PATH="$HOME/.guix-profile/lib/gtk-3.0" -export GI_TYPELIB_PATH="$HOME/.guix-profile/lib/girepository-1.0" -export XDG_DATA_DIRS="$HOME/.guix-profile/share" -export GIO_EXTRA_MODULES="$HOME/.guix-profile/lib/gio/modules" -#+end_src bash - -run the main script (in ~/.guix-profile/bin) - -#+begin_src bash -genenetwork2 -#+end_src bash - -will start the default server which listens on port 5003, i.e., -http://localhost:5003/. - -OK, we are where we were before with step 4. Only difference is that we -used our own compiled guix server. +See [[development.org]]. * Trouble shooting @@ -479,6 +220,31 @@ 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). +** Mysql can't connect server through socket ERROR + +The following error + +: sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2002, 'Can\'t connect to local MySQL server through socket \'/run/mysqld/mysqld.sock\' (2 "No such file or directory")') + +means that MySQL is trying to connect locally to a non-existent MySQL +server, something you may see in a container. Typically replicated with something like + +: mysql -h localhost + +try to connect over the network interface instead, e.g. + +: mysql -h 127.0.0.1 + +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 + +* 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. + * IRC session Here an IRC session where we installed GN2 from scratch using GNU Guix diff --git a/doc/development.org b/doc/development.org new file mode 100644 index 00000000..bbb6084f --- /dev/null +++ b/doc/development.org @@ -0,0 +1,23 @@ +* Development + +After cloning the git source tree you can run the contained GN2 using +an existing GN2_PROFILE, i.e., use a profile that was create to run a +binary installation of GN2. This profile may be found by typing + +: which genenetwork2 +: /home/wrk/opt/gn-latest-guix/bin/genenetwork2 + +An example of running the development version would be + +: env GN2_PROFILE=/home/wrk/opt/gn-latest-guix ./bin/genenetwork2 + +Profiles are stored in /gnu/store, so you may pick one up there + +: readlink -f $(dirname $(dirname `which genenetwork2`)) +: /gnu/store/dvckpaw770b00l6rv4ijql8wrk11iypv-profile + +and use that instead. + +Note that the genenetwork2 script sets up the environment for running +the webserver. This includes path to R modules and python modules. These +are output on startup. To make sure there is no environment pollution you can -- cgit v1.2.3 From 755b9aaa31c73cc5fe8c1a75d74846f1d8594419 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 31 May 2017 07:12:28 +0000 Subject: JS module handling --- VERSION | 2 +- bin/genenetwork2 | 2 +- doc/development.org | 20 ++++++++++++++++++++ etc/default_settings.py | 2 +- wqflask/utility/tools.py | 37 +++++++++++++++++++++++++++++-------- wqflask/wqflask/views.py | 6 +++--- 6 files changed, 55 insertions(+), 14 deletions(-) (limited to 'doc') diff --git a/VERSION b/VERSION index 144b089a..3e0b7cab 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.10-pre1 +2.10-pre4 diff --git a/bin/genenetwork2 b/bin/genenetwork2 index df688989..b3190f1e 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -68,7 +68,7 @@ else export PATH=$GN2_PROFILE/bin:$PATH export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages export R_LIBS_SITE=$GN2_PROFILE/site-library - export GUIX_JS_PATH=$GN2_PROFILE/share/genenetwork2/javascript + export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" export XDG_DATA_DIRS="$GN2_PROFILE/share" diff --git a/doc/development.org b/doc/development.org index bbb6084f..5e6e318b 100644 --- a/doc/development.org +++ b/doc/development.org @@ -1,5 +1,7 @@ * Development +** Using GN2_PROFILE + After cloning the git source tree you can run the contained GN2 using an existing GN2_PROFILE, i.e., use a profile that was create to run a binary installation of GN2. This profile may be found by typing @@ -21,3 +23,21 @@ and use that instead. Note that the genenetwork2 script sets up the environment for running the webserver. This includes path to R modules and python modules. These are output on startup. To make sure there is no environment pollution you can + +** Javascript modules + +As of release 2.10-pre4 we Javascript modules are installed in three places: + +1. JS_GUIX_PATH: the Guix store - these are Guix pre-packaged modules +2. The git source tree (./wqflask/wqflask/static/packages/) +3. JS_GN_PATH: a local directory containing (temporary) development modules + +Packages currently in git (2) will move to JS_GUIX_PATH (1) over +time. This is to keep better track of origin updates. Putting packages +in git (2) is actively discouraged(!), unless there are GN2 specific +adaptations to the original Javascript modules. + +JS_GN_PATH (3) is for development purposes. By default is is set to +$HOME/genenetwork/javascript. Say you are working on an updated +version of a JS module not yet in (1) you can simply check out that +module in that path and it should show up. diff --git a/etc/default_settings.py b/etc/default_settings.py index 4f3a6f5c..1c5b10b4 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -61,7 +61,7 @@ HOME = os.environ['HOME'] # PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused) # ---- Local path to JS libraries - for development modules (only) -# GN2_JS_PATH = os.environ['HOME']+"/genenetwork/javascript" (unused) +JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript" # ---- GN2 Executables (overwrite for testing only) # PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index d46a84ba..c1c6fd36 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -13,6 +13,11 @@ logger = logging.getLogger(__name__ ) OVERRIDES = {} +def app_set(command_id, value): + """Set application wide value""" + app.config.setdefault(command_id,value) + value + def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in app.config, with valid_path is a function checking whether the @@ -40,6 +45,7 @@ def get_setting(command_id,guess=None): def value(command): if command: # sys.stderr.write("Found "+command+"\n") + app_set(command_id,command) return command else: return None @@ -89,6 +95,18 @@ def valid_path(dir): return dir return None +def js_path(module=None): + """ + Find the JS module in the two paths + """ + try_gn = get_setting("JS_GN_PATH")+"/"+module + if valid_path(try_gn): + return try_gn + try_guix = get_setting("JS_GUIX_PATH")+"/"+module + if valid_path(try_guix): + return try_guix + raise "No JS path found for "+module+" (check JS_GN_PATH)" + def pylmm_command(guess=None): return valid_bin(get_setting("PYLMM_COMMAND",guess)) @@ -212,16 +230,19 @@ USE_REDIS = get_setting_bool('USE_REDIS') USE_GN_SERVER = get_setting_bool('USE_GN_SERVER') GENENETWORK_FILES = get_setting('GENENETWORK_FILES') -GUIX_JS_PATH = get_setting('GUIX_JS_PATH') -assert_dir(GUIX_JS_PATH) - -PYLMM_COMMAND = pylmm_command() -GEMMA_COMMAND = gemma_command() -PLINK_COMMAND = plink_command() +JS_GUIX_PATH = get_setting('JS_GUIX_PATH') +assert_dir(JS_GUIX_PATH) +JS_GN_PATH = get_setting('JS_GN_PATH') +assert_dir(JS_GN_PATH) + +PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) +GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) TEMPDIR = tempdir() # defaults to UNIX TMPDIR -TWITTER_POST_FETCHER_JS_PATH = GUIX_JS_PATH + "/Twitter-Post-Fetcher" -assert_dir(TWITTER_POST_FETCHER_JS_PATH) +# ---- Handle specific JS modules +JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("Twitter-Post-Fetcher")) +assert_dir(JS_TWITTER_POST_FETCHER_PATH) from six import string_types diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3882e60a..07151425 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -53,7 +53,7 @@ from wqflask.ctl import ctl_analysis #from wqflask.trait_submission import submit_trait from utility import temp_data -from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,TWITTER_POST_FETCHER_JS_PATH +from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH from utility.helper_functions import get_species_groups from base import webqtlFormData @@ -147,8 +147,8 @@ def tmp_page(img_path): img_base64 = bytesarray ) @app.route("/twitter/") -def bd_files(filename): - return send_from_directory(TWITTER_POST_FETCHER_JS_PATH, filename) +def twitter(filename): + return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) #@app.route("/data_sharing") #def data_sharing_page(): -- cgit v1.2.3