path: root/doc/README.org

#+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 ]]
 - [[#source-deployment][Source deployment]]
   - [[#update-guix][Update guix]]
   - [[#install-gn2][Install GN2]]
   - [[#run-gn2][Run GN2]]
   - [[#run-mysql-server][Run MySQL server]]
   - [[#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]]
 - [[#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]]

* Introduction

Large system deployments can get very 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]].

* 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 section on [[#run-mysql-server][Run
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 recipe!

* Source deployment

This section gives a more elaborate instruction for installing GN2
from source.

First execute above 3 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]]

** Update guix

Instead of Step 4 we now compile Guix from scratch.

Create, install and run a recent version of the guix-daemon by
compiling the guix repository. Follow [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][these]] steps carefully.

** Install GN2

#+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!

Here an IRC session where we installed GN2 from scratch using GNU Guix
and a download of the test database:

#+begin_src
<pjotrp> time to get binary install sorted :)  [07:03]
<pjotrp> Guix is designed for distributed installation servers
<pjotrp> we have one on guix.genenetwork.org
<pjotrp> it contains all the prebuild packages
<pjotrp> for GN
<user01> okay  [07:04]
<pjotrp> let's step back however  [07:05]
<pjotrp> I presume the environment is set with all guix package --search-paths
<pjotrp> right?
<user01> yep
<user01> set to the ones in ~/.guix-profile/
<pjotrp> good, and you are in gn-latest-guix repo  [07:06]
<user01> yep  [07:07]
<pjotrp> git log shows 

Author: David Thompson <dthompson2@worcester.edu>
Date:   Sun Mar 27 21:20:19 2016 -0400

<user01> yes
<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix
         package -A genenetwork2  [07:08]
<pjotrp> 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

<user01> yeah  [07:09]
<pjotrp> OK, we are in sync. This means we should be able to install the exact
         same software
<pjotrp> I need to start up my guix daemon - I usually run it in a screen
<pjotrp> screen -S guix-daemon
<user01> hah, I don't have screen installed yet  [07:11]
<pjotrp> comes with guix ;)  [07:12]
<pjotrp> no worries, you can run it any way you want
<pjotrp> $HOME/.guix-profile/bin/guix-daemon --build-users-group=guixbuild 
<user01> then something's weird, because it says I don't have it
<pjotrp> oh, you need to install it first  [07:13]
<pjotrp> guix package -A screen
<pjotrp> screen  4.3.1   out     gnu/packages/screen.scm:34:2
<pjotrp> but you can skip this install, for now
<user01> alright  [07:14]
<pjotrp> env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix
         package -i genenetwork2 --dry-run
<pjotrp> substitute: updating list of substitutes from
         'https://mirror.hydra.gnu.org'...  79.1%
<pjotrp> you see that?
<pjotrp> 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

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

** 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/.

** Run MySQL server

At this point we require the underlying distribution to install
and run mysqld. 

Download one of

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 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.

** 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]].

* 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.