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-rw-r--r--doc/README.org16
1 files changed, 10 insertions, 6 deletions
diff --git a/doc/README.org b/doc/README.org
index 86c8faaa..1894d8d3 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -24,7 +24,6 @@ checked out version of the Guix package tree (this is required for
reproducibility).
* Source deployment
-
** Install guix
Deploying from source is also straightforward. Install GNU Guix using
@@ -43,7 +42,7 @@ repositories:
cd ~
mkdir genenetwork
cd genenetwork
-git clone https://github.com/genenetwork/guix-bioinformatics
+git clone --branch gn-latest https://github.com/genenetwork/guix-bioinformatics
git clone --recursive --branch gn-latest https://github.com/genenetwork/guix guix-gn-latest
cd guix-gn-latest
#+end_src bash
@@ -57,11 +56,13 @@ version of the guix-daemon by compiling the guix repository. Follow
** Install GN2
#+begin_src bash
-export GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/
-cd ~/genenetwork/guix-gn-latest
-./pre-inst-env guix package -i genenetwork2
+env GUIX_PACKAGE_PATH=../guix-bioinformatics/ ./pre-inst-env guix package -i genenetwork2 --fallback
#+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).
+
Make a note of the paths with
#+begin_src bash
@@ -126,6 +127,10 @@ Set permissions and match password in your settings file below:
: mysql> grant all privileges on db_webqtl_s.* to gn2@"localhost" identified by 'mysql_password';
+Note that if the mysql connection is not working, try connecting to
+the IP address and check server firewall, hosts.allow and mysql IP
+configuration.
+
** Run your own copy of GN2
At some point you may want to fix the source code. Clone the GN2
@@ -149,7 +154,6 @@ and everything *should* work (note the full path to the settings
file). This way we develop against the exact same dependency graph of
software.
-
* Source deployment and other information on reproducibility
See the document [[GUIX-Reproducible-from-source.org]].