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authorzsloan2017-01-26 13:43:10 -0600
committerGitHub2017-01-26 13:43:10 -0600
commit298ca525114a570794d4326613be54ec223dce8b (patch)
tree1e0c445912af7ccb273a25b858889048eb96f756 /doc
parente63c4014e7bc34b440707be19af3779b72102fdb (diff)
parent7ea8ee22074c297925335cc048777f0ce8cb3912 (diff)
downloadgenenetwork2-298ca525114a570794d4326613be54ec223dce8b.tar.gz
Merge pull request #1 from genenetwork/testing
Various changes/fixes
Diffstat (limited to 'doc')
-rw-r--r--doc/README.org48
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>