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authorPjotr Prins2016-03-05 16:45:06 +0000
committerPjotr Prins2016-04-20 10:07:44 +0000
commit87442be548c8779bcc06693490b9e11ccba26dc5 (patch)
tree66080f1362b7e1a26b2790b156ee785626085a89 /doc
parentd8b3b06ada09b7aeead3a179673c3121d786ad46 (diff)
downloadgenenetwork2-87442be548c8779bcc06693490b9e11ccba26dc5.tar.gz
README
Diffstat (limited to 'doc')
-rw-r--r--doc/README.org21
1 files changed, 12 insertions, 9 deletions
diff --git a/doc/README.org b/doc/README.org
index adb545f6..ec0054e4 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -5,10 +5,11 @@
- [[#source-deployment][Source deployment]]
- [[#install-guix][Install guix]]
- [[#checkout-the-git-repositories][Checkout the git repositories]]
+ - [[#update-guix][Update guix]]
+ - [[#update-the-path][Update the path]]
- [[#install-gn2][Install GN2]]
- [[#run-gn2][Run GN2]]
- [[#run-mysql-server][Run MySQL server]]
- - [[#notes][Notes]]
- [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]]
* Introduction
@@ -47,9 +48,15 @@ git clone --recursive --branch gn-latest https://github.com/genenetwork/guix gui
cd guix-gn-latest
#+end_src bash
-*** Update the path
+** Update guix
-Now make sure the guix update path is inline with ours
+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.
+
+** Update the path
+
+Now make sure the guix update path is in line with ours
#+begin_src bash
mkdir -p ~/.config/guix
@@ -60,7 +67,8 @@ ln -s ~/genenetwork/guix-gn-latest ~/.config/guix/latest
#+begin_src bash
export GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/
-guix package -i genenetwork2
+cd ~/genenetwork/guix-gn-latest
+./pre-inst guix package -i genenetwork2
#+end_src bash
** Run GN2
@@ -107,11 +115,6 @@ 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';
-** Notes
-
-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.
* Source deployment and other information on reproducibility