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diff --git a/doc/README.org b/doc/README.org index ecc9b799..adb545f6 100644 --- a/doc/README.org +++ b/doc/README.org @@ -2,19 +2,13 @@ * Table of Contents :TOC: - [[#introduction][Introduction]] - - [[#binary-deployment][Binary deployment]] - - [[#install-guix-using-a-tar-ball][Install Guix using a tar ball]] - - [[#fix-locale][Fix locale]] - - [[#authorize-our-archives][Authorize our archives]] - - [[#download-and-install-the-gn2-archive][Download and install the GN2 archive]] - [[#source-deployment][Source deployment]] - [[#install-guix][Install guix]] - [[#checkout-the-git-repositories][Checkout the git repositories]] - - [[#run-guix-daemon][Run guix-daemon]] - [[#install-gn2][Install GN2]] - [[#run-gn2][Run GN2]] - [[#run-mysql-server][Run MySQL server]] - - [[#other][Other]] + - [[#notes][Notes]] - [[#source-deployment-and-other-information-on-reproducibility][Source deployment and other information on reproducibility]] * Introduction @@ -24,94 +18,9 @@ explain the GeneNetwork 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 system can be used to install GN with all its files and dependencies. -* Binary deployment - -Note binary deployment is not working pending a few improvements -to GNU Guix. See source deployment instead. - -** Install Guix using a tar ball - -GN can be deployed either as a binary tarball or as a GNU Guix -package. First install GNU Guix following the instructions of the -[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html#Binary-Installation][binary installation]] using a tar ball from [[https://www.gnu.org/software/guix/download/][here]]. - -With guix-daemon running you should be able to install the hello -package: - -: guix package -i hello - -** Fix locale - -You may want to - -#+begin_src sh :lang bash -export GUIX_LOCPATH=$HOME/.guix-profile/lib/locale -export LC_ALL=en_US.utf8 -#+end_src sh :lang bash - -** Authorize our archives - -Next add our archive key to guix (as root): - -#+begin_src scheme -echo "(public-key - (ecc - (curve Ed25519) - (q #E9A95686D8437186302E07C7AB9BF3913F435026C2D389AF27D9C66FD6EBB649#) - ) - ) -"|guix archive --authorize -#+end_src scheme - -if you have trouble finding a suitable guix try - -: ls /gnu/store/*guix-*/bin/guix - -and you should be able to use this directly, e.g. - -: alias guix=/gnu/store/632msbms2yaldfnlrb5lbnlnmn9yjisw-guix-0.9.0/bin/guix -: guix --version - -** Download and install the GN2 archive - -Find the archive on - - http://files.genenetwork.org/software/ - -download and install with - -#+begin_src bash -guix archive --import < genenetwork2-data-hash.nar -#+end_src bash - -and you should see a list of packages installing, e.g. - -#+begin_src bash -importing path `/gnu/store/l1zs2drn3zdzl5ysjcmhibcpa35p9zfc-python2-mysqlclient-1.3.7' -importing path `/gnu/store/n7kfg4knibvblggy8ci2liscl7vz5wkg-python2-parallel-1.6.4' -importing path `/gnu/store/qvv16qwlq59gp5d07lwbf5n8ndsi3il3-python2-sqlalchemy-1.0.11' -importing path `/gnu/store/qw872mbmr9ir0a9drv9xw9pvjk05ywwy-python2-xlsxwriter-0.8.4' -importing path `/gnu/store/wc112m1xfy3p08v14bdzay2ki2rirdsm-pylmm-gn2-1.0-3c6d1cac8' -importing path `/gnu/store/zfkcy17c2ks3cd9ks14irdabqvmlfpyn-python2-flask-sqlalchemy-2.1' -importing path `/gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff4' -(etc.) -#+end_src bash - -The following packages need to be added and the R path set - -: export R_LIBS_SITE="/home/wrk/.guix-profile/site-library/" -: guix package -i /gnu/store/w0dqg9dshq53j8xhcnqgvnvms2s6y5k5-r-wgcna-1.49-425bc170cc0873ddbd414675ac40f6d4d724c7cb -: guix package -i /gnu/store/k60bdlm0v7xic88j2z5c1jb1jvc371mn-r-qtl-1.38-4 - -You can add the last one to your profile - -: guix package -i /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff -: export PATH=~/.guix-profile/bin:$PATH -: genenetwork2 - - or run it directly with - -: /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff/bin/genenetwork2 +The official installation path is via a GNU Guix installation from a +checked out version of the Guix package tree (this is required for +reproducibility). * Source deployment @@ -120,9 +29,14 @@ You can add the last one to your profile Deploying from source is also straightforward. Install GNU Guix using a binary tar ball as described [[https://github.com/pjotrp/guix-notes][here]]. +If it works you should be able to install a package with + +: guix package -i hello + ** Checkout the git repositories -Check out the guix and guix-bioinformatics repositories: +Check out the two relevant guix and guix-bioinformatics git +repositories: #+begin_src bash cd ~ @@ -133,17 +47,20 @@ git clone --recursive --branch gn-latest https://github.com/genenetwork/guix gui cd guix-gn-latest #+end_src bash -** Run guix-daemon +*** Update the path -At this 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. +Now make sure the guix update path is inline with ours + +#+begin_src bash +mkdir -p ~/.config/guix +ln -s ~/genenetwork/guix-gn-latest ~/.config/guix/latest +#+end_src bash ** Install GN2 #+begin_src bash -env GUIX_PACKAGE_PATH=../guix-bioinformatics/ \ - ./pre-inst-env guix package -i genenetwork2 +export GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ +guix package -i genenetwork2 #+end_src bash ** Run GN2 @@ -190,22 +107,11 @@ 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 -** Other - -Update guix with a 'guix pull' and make guix visible in the path. -More information exists also in my [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org][guix-notes]]. - -With guix running you should be able to install python, for example. - -: guix package -i python2 - -This will make python appear in $HOME/.guix-profile/bin/python. Suggested -environment settings can be seen with - -: guix package --search-paths - - +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 |