Added IRC log

1 files changed, 409 insertions, 6 deletions

diff --git a/doc/README.org b/doc/README.org
index 9608548d..9fa44442 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -68,9 +68,415 @@ env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env \
 #+end_src bash
 
 Note that you can use the genenetwork.org guix substitute caching
-server at http://guix.genenetwork.org (which speeds up installs
-significantly because all packages are pre-built). And/or use the Guix
-mirror with option --substitute-urls=http://mirror.guixsd.org
+server at http://guix.genenetwork.org:8080 (which speeds up installs
+significantly because all packages are pre-built). Here an IRC session
+where we installed GN2 from scratch using GNU Guix and a download
+of the test database:
+
+#+begin_src bash
+<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 bash
+
+** Run GN2
 
 Make a note of the paths with
 
@@ -78,8 +484,6 @@ Make a note of the paths with
 ./pre-inst-env guix package --search-paths
 #+end_src bash
 
-** Run GN2
-
 After setting the paths for the server
 
 #+begin_src bash
@@ -196,7 +600,6 @@ 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