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diff --git a/doc/README.org b/doc/README.org index 278dd31c..f49143af 100644 --- a/doc/README.org +++ b/doc/README.org @@ -3,9 +3,12 @@ * 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]] - - [[#install-guix][Install guix]] - - [[#checkout-the-git-repositories][Checkout the git repositories]] - [[#update-guix][Update guix]] - [[#install-gn2][Install GN2]] - [[#run-gn2][Run GN2]] @@ -30,20 +33,69 @@ 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]]. -* Source deployment -** Install guix +* 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]]. + +** Step 1: Install GNU Guix + +Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow +[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially download and unpack the tar ball (which +creates directories in /gnu and /var/guix), add build users and group +(Guix builds software as unpriviliged users) and run the Guix daemon +after fixing the paths (aka known as the 'profile'). + +You have succeeded and you have set the [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting +permission to download binaries), you should be able to install the +hello package using binary install + +: export PATH=~/.guix-profile/bin:$PATH +: guix pull +: guix package -i hello --dry-run -Deploying from source is also straightforward. Install GNU Guix using -a binary tar ball as described [[https://github.com/pjotrp/guix-notes][here]]. +Which should show something like -If it works you should be able to install a package with +: The following files would be downloaded: +: /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10 +: ... + +where 'downloaded' means binary installs. The actual installation +command of 'hello' is : guix package -i hello +: hello +: Hello, world! + +If you 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'. + +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]]. + +Probably a good idea to update guix to the latest + +: guix pull +: guix package -i guix +: guix --version +: guix (GNU Guix) 0.10.0 -** Checkout the git repositories +and then best restart the daemon (see above). -Check out the two relevant guix and guix-bioinformatics git -repositories: +** 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 + +: guix package -i git +: export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt + +check out the git repsitories (gn-latest branch) #+begin_src bash cd ~ @@ -54,24 +106,87 @@ git clone --branch gn-latest --recursive https://github.com/genenetwork/guix gui 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 + +: guix archive --authorize + +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: + +: rm /root/.config/guix/latest +: ln -s ~/genenetwork/guix-gn-latest/ /root/.config/guix/latest + +Now check whether you can find the GN2 package with + +: env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2 +: genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2 + +(ignore the source file newer then ... messages, this is caused by the +/root/.config/guix/latest override). + +And install with + +: env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org:8080 https://mirror.guixsd.org" + +After installation you should be able to run genenetwork2 + +: genenetwork2 + +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 -At some point you may decide to 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. +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=../guix-bioinformatics/ ./pre-inst-env \ - guix package -i genenetwork2 --fallback +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 that you can use the genenetwork.org guix substitute caching -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: +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] |