#+TITLE: Installing GeneNetwork services * 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 ]] - [[#run-mysql-server][Run MySQL server]] - [[#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]] - [[#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]] - [[#irc-session][IRC session]] * Introduction Large system deployments can get very [[http://biobeat.org/gn2.svg][complex]]. In this document we explain the GeneNetwork version 2 (GN2) reproducible deployment system which is based on GNU Guix (see also Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]). The Guix 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]]. 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. ** 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 you have to 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 repsitories (gn-latest branch) #+begin_src bash cd ~ mkdir genenetwork cd genenetwork git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics git clone --branch gn-latest --recursive https://github.com/genenetwork/guix guix-gn-latest cd guix-gn-latest #+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-latest/ /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:8080 https://mirror.guixsd.org" \ --fallback #+end_src Note that you may (currently) get an error: : guix substitute: error: download from 'http://guix.genenetwork.org:8080/nar/sqd3q1xq5fsbga00bwhghi9shi7xdaac-gtk+-3.18.2' failed: 404, "Not Found" which can be fixed with using the --fallback switch, or install : guix package -i gtk+@3.18.2 and restart the genenetwork2 install. After installation you should be able to run genenetwork2 after updating the Guix suggested environment vars. Check the ouput 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 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! * Run MySQL server At this point we require the underlying distribution to install and run mysqld. 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 Check the md5sum. After installation inflate the database binary in the MySQL directory (this installation path is subject to change soon) : 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 : mysql> show databases; : +--------------------+ : | Database | : +--------------------+ : | information_schema | : | db_webqtl_s | : | mysql | : | performance_schema | : +--------------------+ 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'; 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. 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. * GN2 Dependency Graph Graph of all runtime dependencies as installed by GNU Guix. #+ATTR_HTML: :title GN2_graph [[http://biobeat.org/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 : 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-latest 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:8080 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 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. * Trouble shooting ** ImportError: No module named jinja2 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: : guix package --search-paths On one system: : export PYTHONPATH="$HOME/.guix-profile/lib/python2.7/site-packages" : export R_LIBS_SITE="$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 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). ** 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. * IRC session Here an IRC session where we installed GN2 from scratch using GNU Guix and a download of the test database. #+begin_src time to get binary install sorted :) [07:03] Guix is designed for distributed installation servers we have one on guix.genenetwork.org it contains all the prebuild packages for GN okay [07:04] let's step back however [07:05] I presume the environment is set with all guix package --search-paths right? yep set to the ones in ~/.guix-profile/ good, and you are in gn-latest-guix repo [07:06] yep [07:07] git log shows Author: David Thompson Date: Sun Mar 27 21:20:19 2016 -0400 yes env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -A genenetwork2 [07:08] shows genenetwork2 2.0-a8fcff4 out ../guix-bioinformatics/gn/packages/genenetwork.scm:144:2 genenetwork2-database-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:270:4 genenetwork2-files-small 1.0 out ../guix-bioinformatics/gn/packages/genenetwork.scm:228:4 yeah [07:09] OK, we are in sync. This means we should be able to install the exact same software I need to start up my guix daemon - I usually run it in a screen screen -S guix-daemon hah, I don't have screen installed yet [07:11] comes with guix ;) [07:12] no worries, you can run it any way you want $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild then something's weird, because it says I don't have it oh, you need to install it first [07:13] guix package -A screen screen 4.3.1 out gnu/packages/screen.scm:34:2 but you can skip this install, for now alright [07:14] env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2 --dry-run substitute: updating list of substitutes from 'https://mirror.hydra.gnu.org'... 79.1% you see that? followed by [07:15] substitute: updating list of substitutes from 'https://hydra.gnu.org'... 100.0% The following derivations would be built: /gnu/store/rk7nw0rjqqsha958m649wrykadx6mmhl-profile.drv /gnu/store/7b0qjybvfx8syzvfs7p5rdablwhbkbvs-module-import-compiled.drv /gnu/store/cy9zahbbf23d3cqyy404lk9f50z192kp-module-import.drv /gnu/store/ibdn603i8grf0jziy5gjsly34wx82lmk-gtk-icon-themes.drv which should have the same HASH values /gnu/store/7b0qjybvf... etc. [07:16] profile has a different hash but the next ones? they're the same not sure why profile differs. Do you see the contact with mirror.hydra.org? [07:17] yeah OK, that means you set the key correctly for that one :) alright we are at the same state now. You can see most packages need to be rebuild because they are no longer cached as binaries on hydra [07:18] things move fast... hehe let me also do the same on my laptop - which I have staged before [07:19] btw, to set the path I often do [07:20] export PATH="/home/wrk/.guix-profile/bin:/home/wrk/.guix-profile/sbin":$PATH to keep things like 'screen' from Debian Once past building guix itself that is normally OK [07:21] ah, okay will do that the guix build requires certain versions of tools, so you don't want to mix foreign tools in [07:23] makes sense [07:24] On my laptop I am trying the main updating list of substitutes from 'http://hydra.gnu.org'... 10.5% [07:27] it is a bit slow, but let's see if there is a difference with the mirror you can see there are two servers here. Actually with recent daemons, if the mirror fails it will try the main server [07:28] I documented the use of a caching server here [07:29] https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org this is exactly what we are doing now alrighty [07:35] To see if a remote server has a guix server running it should respond [07:36] lynx http://guix.genenetwork.org:8080 --dump Resource not found: / you see that? yes [07:37] good. The main hydra server is too slow. So on my laptop I forced using the mirror with [07:38] env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --dry-run --substitute-urls="http://mirror.hydra.gnu.org" the list looks the same to me [07:40] me too note that some packages will be built and some downloaded, right? [07:41] yes atlas is actually a binary on my system [07:43] I mean in that list so, it should not build. Same as yours? yeah, atlas and r-gtable are the ones to be downloaded You should not have seen that error ;) we should try and install it this way, try [07:44] env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2 --cores=4 --max-jobs=4 --keep-going [07:46] set CPUs and max-jobs to something sensible Does your VM have multiple cores? note you can always press Ctrl-C during install it doesn't, I'll reboot it and give it another core [07:47] Hey [07:48] I'm here Will be stepping away for some breakfast Can you do the same as us Can you see the irc log Alright Yes, I can Please email me a copy in five minutes user01: so when I use the GN server [07:56] env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2 --dry-run --substitute-urls=http://guix.genenetwork.org:8080 I don't need to build anything [07:57] (this won't work for you, yet) to get it to work you need to 'trust' it [07:58] but, first get the build going I'll have a coffee while you and get building yeah it's doing its thing now [08:01] cool [08:02] in a separate terminal you can try and install with the gn mirror [08:05] I'll send you the public key and you can paste it as said https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org [08:06] alright should be in the E-mail [08:09] getting it working it kinda nasty since the server gives no feedback it works when you see no more in the build list ;) [08:11] btw, you can install software in parallel. Guix does that. even the same packages so keep building ;) try and do this with Debian... coffee for me [08:12] the first build failed [08:15] OK, Dennis fixed that one yesterday [08:27] the problem is that sometime source tarballs disappear [08:28] R is notorious for that haha, that's inconvenient.. well, it is good that Guix catches them but we do not cache sources binaries are cached - to some degree - so we don't have to rebuild those [08:29] time to use the guix cache at guix.genenetwork.org try and install the key (it is in the E-mail) and see what this lists [08:31] env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -i genenetwork2 --substitute-urls=http://guix.genenetwork.org:8080 --dry-run should be all binary installs it's not.. [08:32] if I remove --substitute-urls, the list changes, does that mean I have the key set up correctly at least? [08:33] dunno [08:35] how many packages does it want to build? should be zero four Ah, that is OK - those are default profile things genenetwork2 is among the ones to be downloaded so [08:36] remove --dry-run yeah, good sign :) we'll still hit a snag, but run it should be fast doing it [08:37] it worked! [08:38] I think [08:39] heh [08:40] you mean it is finished? yep type genenetwork2 complains about not being able to connect to the database [08:41] last snag :) no database well, we succeeded in installing a same-byte install of a very complex system :) [08:42] (always take time to congratulate yourself) now we need to install mysql hehe :) this can be done throug guix or through debian [08:43] the latter is a bit easier here, so let's do that fun note: you can mix debian and guix Follow instructions on [08:44] https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-mysql-server apt-get install mysql-common [08:45] may do it You can also install with guix, but I need to document that btw your internet must be fast :) [08:46] hehe it is ;) when the database is installed [08:48] be sure to set the password as instructed [08:50] when mysql is set the genenetwork2 command should fire up the web server on localhost:5003 [08:58] btw my internet is way slower :) [09:00] I'm back [09:04] fixed router firmware upgrade problem unbricking tssk [09:07] I'll never leave routers to update themselves again [09:08] self-brick highway Resuming [09:09] auto-updates are evil always switch them off user02: can you install genenetwork like user has done? [09:10] pretty well documented here now :) Yes I can [09:11] Already installed key user02: you are getting binary packages only now? [09:13] That's the sanest way to go now seriously everything should be pre-built from guix.genenetwork.org you are downloading? yes [09:15] cool. Maybe an idea to set up a server for your own use Stuck at downloading preprocesscore should not [09:24] what does env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org:8080" --dry-run [09:25] say for r-prepocesscore download or build? mine says download [09:26] it only lists the derivatives to be built nothing else happens [09:27] OK, so there is a problem your key may not be working everything should be listed as 'to be download' [09:28] Hmm Ah I know where I messed up where? I did add the key However (I am documenting) I did not tell guix to trust it yes and there is another potential problem Remember the documentation on installing guix? You have to tell guix to trust the default key [09:29] Right? So in this case read the IRC log That step is mandatory user01: how are you doing? user02: https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org#using-gnu-guix-archive [09:30] a little bit left on the db download user02: you should see no more building user02: another issue may be that you updated r-preprocesscore package in guix-buinformatics [09:32] all downstream packages will want to rebuild no, not really It's not even installed checkout a branch of the the old version - make sure we are in synch should be at /gnu/store/y1f3r2xs3fhyadd46nd2aqbr2p9qv2ra-r-biocpreprocesscore-1.32.0 [09:33] pjotrp: Possibly we should use the archive utility of Guix to do deployment to avoid such out-of-sync differences :) [09:34] maybe. I did not get archive to update profiles properly [09:37] Also it is good that they get to understand guix this way carved in stone, eh [09:38] Yeah, all good [09:39] My mistake was skipping the guix archive part Can we begin with the install? It's telling me of derivatives that will be downloaded [09:40] So we're good Here goes yeeha [09:42] pjotrp, where is this guix.genenetwork.org located at? Tennessee It's...it's....sloooooooowwwwwwwwwwwwww not from Europe is it downloading at all? It should be extended Yes...like at 100KB/s [09:43] tear-jerker Verizon problems who's the host? I am getting 500Kb/s UT Guix's servers can run off more than one server, right? I'd like to host that particular server here For speed yes Sooner or later It will be a necessity [09:45] exactly what I am doing - this is our server guix.genenetwork.org:8080 All done installing [09:46] what? Now the databases what do you mean by slow exactly? Yes, it's installed can you run genenetwork2 setting variables If I try running it now, it will fail as I don't have the DBs [09:47] cool - you had a lot of prebuilt packages already OK, follow the instructions I wrote above now everything seems to be working for me :) OK user01: excellent! you see a webserver? yep, can connect to localhost:5003 [09:48] So now you are running a guix copy of GN2 you can see where it lives with `which genenetwork2` or ls -l ~/.guix-profile/bin/genenetwork2 [09:49] /gnu/store/1kma5xszvzsvmbb4k699h7gvdncw901i-genenetwork2-2.0-a8fcff4/bin/genenetwork2 it is a script written by guix, open it [09:50] inside it points to paths and our script at /gnu/store/1kma5xszvzsvmbb4k699h7gvdncw901i-genenetwork2-2.0-a8fcff4/bin/.genenetwork2-real if you open that you can see how the webserver is started [09:51] next step is to run a recent version of GN2 okay [09:52] See https://github.com/genenetwork/genenetwork2/tree/staging/doc#run-your-own-copy-of-gn2 but do not checkout that genetwork2_diet we reverted to the main tree clone git@github.com:genenetwork/genenetwork2.git [09:53] instead and checkout the staging branch that is effectively my branch [09:54] when that is done you should be able to fire up the webserver from there [09:55] using ./bin/genenetwork2 now installing DBs Downloading annoyingly the source tree is ~700Mb [09:56] Can it also be done by installing the guix package genenetwork2-database-small? I changed it in the diet version to 8Mb, but I had to revert I need to make my VM bigger... user02: not ready [09:57] ok user01: sorry user01: you could mount a local dir inside the VM for development that would allow you to use MAC tools for editing just an idea yeah, I figure I'll do something like that do you use emacs? [09:58] yep that can also run on remote files over ssh that's an alternative kudos for using emacs :), wdyt user03 79 minutes to go downloading the db user02: sorry about that [09:59] it is 2GB user, you can also mount the directory via sshfs Mac OSX runs OpenSSH user02: sopa You can therefore mount a directory outside the VM to the VM via sshfs [10:00] yes, 3 options now That way, you can set up a VM only for it's logic Apps + the OS it runs [10:01] For data, let it reside on physical host accessible via sshfs Use this Arch wiki reference: https://wiki.archlinux.org/index.php/SSHFS I edited that last somewhere in 2015, may have been updated since then alright, cool! [10:04] user01: you are almost done [10:06] I wrote an elixir package for guix :) env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -A elixir --substitute-urls="http://guix.genenetwork.org:8080" [10:08] elixir 1.2.3 out ../guix-bioinformatics/gn/packages/elixir.scm:31:2 I am building it on guix.genenetwork.org right now [10:09] nice [10:10] #+end_src