diff options
| -rw-r--r-- | doc/README.org | 16 | ||||
| -rw-r--r-- | doc/database.org | 2 |
2 files changed, 10 insertions, 8 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]]. diff --git a/doc/database.org b/doc/database.org index 6c079225..af4b30eb 100644 --- a/doc/database.org +++ b/doc/database.org @@ -1,6 +1,4 @@ - github Document reduction issue -- github bio-vcf issue - * GeneNetwork Database |