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Diffstat (limited to 'doc/README.org')
| -rw-r--r-- | doc/README.org | 48 |
1 files changed, 29 insertions, 19 deletions
diff --git a/doc/README.org b/doc/README.org index 0f56914a..b38ea664 100644 --- a/doc/README.org +++ b/doc/README.org @@ -31,7 +31,7 @@ of GN2. Large system deployments can get very [[http://biogems.info/contrib/genenetwork/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 +which is based on GNU Guix (see also [[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 @@ -52,15 +52,16 @@ 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. +database. If you use a virtual machine we recommend to use at least +double. ** 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'). +[[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 (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 @@ -104,17 +105,23 @@ guix package -i git export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt #+end_src -check out the git repsitories (gn-latest branch) +check out the git repositories (gn-deploy 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 +git clone --branch gn-deploy https://github.com/genenetwork/guix-bioinformatics +git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix guix-gn-deploy +cd guix-gn-deploy #+end_src bash +To test whether this is working try: + +#+begin_src bash +#+end_src bash + + ** Step 3: Authorize the GN Guix server GN2 has its own GNU Guix binary distribution server. To trust it you have @@ -146,7 +153,7 @@ 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 +ln -s ~/genenetwork/guix-gn-deploy/ /root/.config/guix/latest #+end_src Now check whether you can find the GN2 package with @@ -164,13 +171,16 @@ 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 + --substitute-urls="http://guix.genenetwork.org" #+end_src Note: the order of the substitute url's may make a difference in speed (put the one first that is fastest for your location and time of day). +Note: if your system starts building or gives an error it may well be +Step 3 did not succeed. The installation should actually be smooth at +this point and only do binary installs (no compiling). + After installation you should be able to run genenetwork2 after updating the Guix suggested environment vars. Check the output of @@ -367,7 +377,7 @@ 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 +: cd ~/genenetwork/guix-gn-deploy Make sure to restart the guix daemon and run guix client from this directory. @@ -377,7 +387,7 @@ directory. 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" +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org" #+end_src bash Note the use of ./pre-inst-env here! @@ -486,7 +496,7 @@ and a download of the test database. <pjotrp> right? <user01> yep <user01> set to the ones in ~/.guix-profile/ -<pjotrp> good, and you are in gn-latest-guix repo [07:06] +<pjotrp> good, and you are in gn-deploy-guix repo [07:06] <user01> yep [07:07] <pjotrp> git log shows @@ -645,7 +655,7 @@ The following derivations would be built: <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 + --substitute-urls=http://guix.genenetwork.org --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 @@ -716,7 +726,7 @@ The following derivations would be built: <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 + --substitute-urls="http://guix.genenetwork.org" --dry-run [09:25] <pjotrp> say for r-prepocesscore <pjotrp> download or build? @@ -869,7 +879,7 @@ The following derivations would be built: <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] + --substitute-urls="http://guix.genenetwork.org" [10:08] <pjotrp> elixir 1.2.3 out ../guix-bioinformatics/gn/packages/elixir.scm:31:2 <pjotrp> |