{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2010/11/22/installing-oscar.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/g30hd-nnd21", "url": "https://chem-bla-ics.linkedchemistry.info/2010/11/22/installing-oscar.html", "title": "Installing Oscar", "content_html": "

About half-way my Oscar project now. I blogged about the Oscar Java API ,\nthe command line utility ,\nand the Taverna plugin \n(all in development). Also, David Jessop joined in, boosting the refactoring.\nThe meeting with the ChEBI team last week was\ngreat too. We worked out details for the use cases, involving Oscar and Lezan’s\nChemicalTagger.

\n\n

Here follow some install instructions to get going. Please give things a try,\neven though we are under heavy development. You can monitor the stability of\nthe code via these Hudson pages for oscar4,\noscar4-cli, ChemicalTagger,\nand others. This continuous building of software\nshould be set up for any scientific code.

\n\n

Requirements\nThe follow the below instructions, you will need a working environment with\na tool to process zip files\n(or equivalent), Java DK,\nand Maven. Having wget makes things easier. Oh,\nand you need a working internet connection.

\n\n

The pattern is otherwise the same for all above tools. I will demonstrate the\nprocess with oscar4-cli.

\n\n

Ubuntu and Debian users can use:

\n\n
sudo aptitude install unzip maven2 \\\\\n  openjdk-6-jdk wget\n
\n\n

Downloading the source\nThe source code for the above tools is all hosted on BitBucket,\nusing the Mercurial version control system.\nHowever, there is no need to worry about that, because BitBucket provides source\ndrops. At this page you can\ndownload a .zip file for the command line utilities, which you can unzip with\nyour favorite tool.

\n\n

If you have wget installed you could do from the command line:

\n\n
wget http://bitbucket.org/egonw/oscar4-cli/get/tip.zip\nunzip tip.zip\n
\n\n

which downloads and unzips the latest version in the repository. (This is where\nmonitoring Hudson comes in; there you can check if there are failing unit tests.)

\n\n

Compiling the code\nWith the source code locally installed, it is same for Maven to come into action.\nAgain, I have no clue how to do this on Windows (other than with Cygwin, which\nevery Windows users should have installed, if a virtual machine with a full\nLinux is no option), but maven should run the ‘assembly:single’\ntarget. Or, from the command line:

\n\n
cd oscar4-cli/\nmvn assembly:assembly\ncp target/oscar4-cli-4.0-SNAPSHOT-jar-with-dependencies.jar \\\\\n  ./oscar4-cli-4.0-SNAPSHOT.jar\n
\n\n

That should do: the created oscar4-cli-4.0-SNAPSHOT.jar can be used now to\nrun the command line utilities .\nActually, it should also do fine for using the Oscar4 Java API .

\n\n

Provide feedback\nWe most welcome feedback, or any kind. Feature requests can be posted here,\nand bug reports here.\nYou can also send email to the oscar3-chem-developers\nmailing list.

\n\n

Update: mvn assembly:assembly should be used instead of mvn assembly:single.

", "summary": "About half-way my Oscar project now. I blogged about the Oscar Java API , the command line utility , and the Taverna plugin (all in development). Also, David Jessop joined in, boosting the refactoring. The meeting with the ChEBI team last week was great too. We worked out details for the use cases, involving Oscar and Lezan’s ChemicalTagger.", "date_published": "2010-11-22T00:10:00+00:00", "date_modified": "2026-10-17T00:00:00+00:00", "tags": ["oscar","textmining"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }