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Diffstat (limited to 'doc')
| -rw-r--r-- | doc/README.org | 415 |
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 |