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authorAndreas Maunz <andreas@maunz.de>2012-10-22 10:38:17 +0200
committerAndreas Maunz <andreas@maunz.de>2012-10-22 10:38:17 +0200
commit6b73ae042116bf7c48cc8f20e97669afc47d2368 (patch)
treebca2d0837a9036a95236fd73fd8da1353b431e3b
parent1a683715a71ad7aff8958fc8c46b09654d4a4c80 (diff)
Minor improvements
-rw-r--r--_posts/2012-08-09-install-opentox-development-environment.md27
-rw-r--r--_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md2
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).