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Diffstat (limited to 'doc/README.org')
| -rw-r--r-- | doc/README.org | 21 |
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 |