From d4def6dd1ac052b7dd1292cedbca3d322e37f399 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 2 Nov 2016 21:50:19 +0000 Subject: Fixing docs --- doc/README.org | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 0f56914a..cf76d7ab 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 @@ -104,15 +105,15 @@ 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-stable 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-stable https://github.com/genenetwork/guix-bioinformatics +git clone --branch gn-stable --recursive https://github.com/genenetwork/guix guix-gn-stable +cd guix-gn-stable #+end_src bash ** Step 3: Authorize the GN Guix server @@ -146,7 +147,7 @@ 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-stable/ /root/.config/guix/latest #+end_src Now check whether you can find the GN2 package with @@ -164,7 +165,7 @@ 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" \ + --substitute-urls="http://guix.genenetwork.org https://mirror.guixsd.org" \ --fallback #+end_src @@ -367,7 +368,7 @@ 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-stable Make sure to restart the guix daemon and run guix client from this directory. @@ -377,7 +378,7 @@ 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 +487,7 @@ and a download of the test database. right? yep set to the ones in ~/.guix-profile/ - good, and you are in gn-latest-guix repo [07:06] + good, and you are in gn-stable-guix repo [07:06] yep [07:07] git log shows @@ -645,7 +646,7 @@ The following derivations would be built: and see what this lists [08:31] 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 should be all binary installs it's not.. [08:32] if I remove --substitute-urls, the list changes, does that mean I @@ -716,7 +717,7 @@ The following derivations would be built: should not [09:24] 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] say for r-prepocesscore download or build? @@ -869,7 +870,7 @@ The following derivations would be built: I wrote an elixir package for guix :) 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] elixir 1.2.3 out ../guix-bioinformatics/gn/packages/elixir.scm:31:2 -- cgit v1.2.3 From 4cd2b9769c726e53fed636c1201b93e752da34f1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 3 Nov 2016 18:32:23 +0000 Subject: Updated to use gn-deploy --- doc/README.org | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index cf76d7ab..9c57953d 100644 --- a/doc/README.org +++ b/doc/README.org @@ -105,15 +105,15 @@ guix package -i git export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt #+end_src -check out the git repositories (gn-stable branch) +check out the git repositories (gn-deploy branch) #+begin_src bash cd ~ mkdir genenetwork cd genenetwork -git clone --branch gn-stable https://github.com/genenetwork/guix-bioinformatics -git clone --branch gn-stable --recursive https://github.com/genenetwork/guix guix-gn-stable -cd guix-gn-stable +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 ** Step 3: Authorize the GN Guix server @@ -147,7 +147,7 @@ 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-stable/ /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 @@ -368,7 +368,7 @@ 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-stable +: cd ~/genenetwork/guix-gn-deploy Make sure to restart the guix daemon and run guix client from this directory. @@ -487,7 +487,7 @@ and a download of the test database. right? yep set to the ones in ~/.guix-profile/ - good, and you are in gn-stable-guix repo [07:06] + good, and you are in gn-deploy-guix repo [07:06] yep [07:07] git log shows -- cgit v1.2.3 From e6528ba528d14320322bcf9694c52879dedc418b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 8 Nov 2016 20:09:36 +0000 Subject: README --- doc/README.org | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) (limited to 'doc') diff --git a/doc/README.org b/doc/README.org index 9c57953d..b38ea664 100644 --- a/doc/README.org +++ b/doc/README.org @@ -116,6 +116,12 @@ git clone --branch gn-deploy --recursive https://github.com/genenetwork/guix gui 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 @@ -165,13 +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 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 -- cgit v1.2.3