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| -rw-r--r-- | doc/README.org | 97 |
1 files changed, 60 insertions, 37 deletions
diff --git a/doc/README.org b/doc/README.org index f49143af..36b7d8f2 100644 --- a/doc/README.org +++ b/doc/README.org @@ -42,58 +42,58 @@ install of Debian 8.3.0 (in KVM) though it should work on any modern Linux distribution (including CentOS). For more elaborate installation instructions see [[#source-deployment][Source deployment]]. +Note that GN2 consists of an approx. 4GB installation including +database. + ** Step 1: Install GNU Guix Fetch the GNU Guix binary from [[https://www.gnu.org/software/guix/download/][here]] (middle panel) and follow -[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially download and unpack the tar ball (which -creates directories in /gnu and /var/guix), add build users and group -(Guix builds software as unpriviliged users) and run the Guix daemon -after fixing the paths (aka known as the 'profile'). +[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html][instructions]]. Essentially you have to download and unpack the tar ball +(which creates directories in /gnu and /var/guix), add build users and +group (Guix builds software as unpriviliged users) and run the Guix +daemon after fixing the paths (also known as the 'profile'). -You have succeeded and you have set the [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting -permission to download binaries), you should be able to install the -hello package using binary install +Once you have succeeded, you have to [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-the-key][set the key]] (getting permission +to download binaries from the GNU server) and you should be able to +install the hello package using binary packages (no building) -: export PATH=~/.guix-profile/bin:$PATH -: guix pull -: guix package -i hello --dry-run +#+begin_src bash +export PATH=~/.guix-profile/bin:$PATH +guix pull +guix package -i hello --dry-run +#+end_src Which should show something like : The following files would be downloaded: : /gnu/store/zby49aqfbd9w9br4l52mvb3y6f9vfv22-hello-2.10 : ... +#+end_src -where 'downloaded' means binary installs. The actual installation -command of 'hello' is +means binary installs. The actual installation command of 'hello' is -: guix package -i hello -: hello -: Hello, world! +#+begin_src bash +guix package -i hello +hello + Hello, world! +#+end_src -If you see things building it means that Guix is not yet properly -installed and up-to-date, i.e., the key is missing or you need to do a -'guix pull'. +If you actually see things building it means that Guix is not yet +properly installed and up-to-date, i.e., the key is missing or you +need to do a 'guix pull'. Press Ctrl-C to interrupt. If you need more help we have another writeup in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#binary-installation][guix-notes]]. To get rid of the locale warning see [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#set-locale][set-locale]]. -Probably a good idea to update guix to the latest - -: guix pull -: guix package -i guix -: guix --version -: guix (GNU Guix) 0.10.0 - -and then best restart the daemon (see above). - ** Step 2: Checkout the GN2 git repositories To fixate the software dependency graph GN2 uses git repositories of Guix packages. First install git if it is missing -: guix package -i git -: export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt +#+begin_src bash +guix package -i git +export GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt +#+end_src check out the git repsitories (gn-latest branch) @@ -122,7 +122,9 @@ to add the following key by pasting it into the command -: guix archive --authorize +#+begin_src bash +guix archive --authorize +#+end_src and hit Ctrl-D. @@ -133,24 +135,45 @@ Now you can use the substitute server to install GN2 binaries. Since this is a quick and dirty install we are going to override the GNU Guix package path by pointing the package path to our repository: -: rm /root/.config/guix/latest -: ln -s ~/genenetwork/guix-gn-latest/ /root/.config/guix/latest +#+begin_src bash +rm /root/.config/guix/latest +ln -s ~/genenetwork/guix-gn-latest/ /root/.config/guix/latest +#+end_src Now check whether you can find the GN2 package with -: env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2 -: genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2 +#+begin_src bash +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -A genenetwork2 + genenetwork2 2.0-a8fcff4 out gn/packages/genenetwork.scm:144:2 +#+end_src (ignore the source file newer then ... messages, this is caused by the /root/.config/guix/latest override). And install with -: env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ guix package -i genenetwork2 --substitute-urls="http://guix.genenetwork.org:8080 https://mirror.guixsd.org" +#+begin_src bash +env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ \ + guix package -i genenetwork2 \ + --substitute-urls="http://guix.genenetwork.org:8080 https://mirror.guixsd.org" \ + --fallback +#+end_src + +Note that you may (currently) get an error: -After installation you should be able to run genenetwork2 +: guix substitute: error: download from 'http://guix.genenetwork.org:8080/nar/sqd3q1xq5fsbga00bwhghi9shi7xdaac-gtk+-3.18.2' failed: 404, "Not Found" -: genenetwork2 +which can be fixed with using the --fallback switch, or install + +: guix package -i gtk+@3.18.2 + +and restart the genenetwork2 install. + +After installation you should be able to run genenetwork2. + +#+begin_src bash +genenetwork2 +#+end_src It will complain that the database is missing. See the section on [[#run-mysql-server][Run MySQL server]] for downloading and installing a MySQL GN2 |