diff options
author | Andreas Maunz <andreas@maunz.de> | 2012-10-22 10:38:17 +0200 |
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committer | Andreas Maunz <andreas@maunz.de> | 2012-10-22 10:38:17 +0200 |
commit | 6b73ae042116bf7c48cc8f20e97669afc47d2368 (patch) | |
tree | bca2d0837a9036a95236fd73fd8da1353b431e3b | |
parent | 1a683715a71ad7aff8958fc8c46b09654d4a4c80 (diff) |
Minor improvements
-rw-r--r-- | _posts/2012-08-09-install-opentox-development-environment.md | 27 | ||||
-rw-r--r-- | _posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md | 2 |
2 files changed, 14 insertions, 15 deletions
diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md index 95fa154..b5e8409 100644 --- a/_posts/2012-08-09-install-opentox-development-environment.md +++ b/_posts/2012-08-09-install-opentox-development-environment.md @@ -38,16 +38,14 @@ Conceptual approach: # Installation -Installation (`development` at the point of writing this = 22/08/2012) is tested with Debian 6.0.5 and Ubuntu 11.04. Installer is available at [github](https://github.com/opentox/install). +Installation (`development` at the point of writing this = 08/2012) tested with Debian 6.0.5 and Ubuntu 11.04. Installer available at [github](https://github.com/opentox/install). -Before starting the installation please check if "sudo" is available (e.g. sudo ls), required for base packages. +Check you can run "sudo" commands (e.g. `sudo ls`), which is required for base packages. Install git: # Install git sudo apt-get install git -Please add your ssh key at github via https://github.com/. You may add your name/email address to the local git config. - -Download, configure and execute the installer. +Add your public key at `https://github.com`. Download, configure and execute the installer: git clone git@github.com:opentox/install.git $HOME/install cd $HOME/install @@ -55,9 +53,9 @@ Download, configure and execute the installer. # First check config.sh with your favorite editor ./install silent -This installation script will prepare your system for the use of `opentox` web services, including installing necessary dependencies, `opentox` config, `raptor`, `rasqal`, `rbenv`, `ruby` and `4store`. +This will prepare the system for opentox web services, including dependencies. -# Install opentox services +# Install OpenTox services Load environment (general) @@ -69,7 +67,7 @@ Load environment (with bash): . $HOME/.opentox/ot-tools.sh otconfig -Next opentox-client and opentox-server will be downloaded and installed. +Download and install opentox-client and opentox-server: for f in opentox-client opentox-server; do git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f @@ -82,7 +80,7 @@ Next opentox-client and opentox-server will be downloaded and installed. cd $OT_PREFIX/opentox-server/bin ./opentox-server-install silent -OpenTox services(algorithm compound dataset feature task opentox-test) and tests will be downloaded and installed. +Download and install services and tests: for f in algorithm compound dataset feature model task opentox-test; do git clone "git@github.com:opentox/$f.git" $OT_PREFIX/$f @@ -96,11 +94,12 @@ OpenTox services(algorithm compound dataset feature task opentox-test) and tests done notify -At this point `opentox` web services have been downloaded, installed and configured. +At this point web services have been downloaded, installed and configured. -# Activate and use ot-tools if you are using bash -NOTE: ot-tools do require the use of bash shell. +# Activate and use ot-tools for bash + +NOTE: ot-tools require bash. Add ot-tools to your .bashrc: @@ -112,7 +111,7 @@ All ot-tools (`otconfig`, `otstart`, `otcheck`, `otreload`, `otkill`) are availa [otstart|otcheck|otreload|otkill] [all|algorithm|compound|dataset|feature| model|task|validation|4store] -`otconfig` is the only command not taking an argument, it sets the environment variables for all services. +`otconfig` is the only command not taking an argument. It sets the environment variables for all services. Start all services and the 4store backend with: @@ -155,4 +154,4 @@ The tests take some time and finish with a short report: Finished tests in 44.690815s, 0.9622 tests/s, 4.4528 assertions/s. 43 tests, 199 assertions, 1 failures, 0 errors, 0 skips -To test one specific service, run its script (`ruby [service_name].rb`) located in `$OT_PREFIX/opentox-test/test`. +To test one specific service, run its script (`ruby [service_name].rb`) in `$OT_PREFIX/opentox-test/test`. diff --git a/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md b/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md index 656c5cb..4ded4dc 100644 --- a/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md +++ b/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md @@ -37,6 +37,6 @@ Example: dataset << [ compound, false, 1.0 ] # save - dataset.save + dataset.put You can find more examples in [opentox-test/test/dataset.rb](https://github.com/opentox/opentox-test/blob/development/test/dataset.rb). |