Launch importing process in background

[Darèios89]

I try from many weeks to import DB but i have not done it. I downloaded all uniprot file from DownloadAndPrepareBio4jSources, but where i have to put them? And when i run the instruction:

sudo jdk1.6.0_23/bin/java -d64 -Xmx30G -jar ExecuteBio4jTool.jar executionsBio4j.xml &

Have i to change directory from the terminal and go where ExecuteBio4jTool.jar file is located? Have i to put executionsBio4j.xml in the same folder? And how the bash importing instruction can find all downloaded files from DownloadAndPrepare......without putting them as parameters of that bash instruction?

[Pablo Pareja Tobes]

Hi Dareios,

You don't have to put the files downloaded anywhere in particular, just make sure they are in the same folder you have the jar file (in case you are not specifying full paths in the executionsBio4j.xml file).

Regarding executionsBio4j.xml file you just need to have it at the same level as ExecuteBio4jTool jar file, (otherwise you would simply need to specify the full path to where the file is located.)

The file executionsBio4j.xml represents the execution of different programs sequentially. Each <execution> tag includes the program parameters inside <argument> tags.

HTH

Cheers,

Pablo

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[Pavan Kumar]

I am trying to import bio4j from the below link:

https://github.com/bio4j/Bio4j/wiki/Importing-bio4j

I am not able to run ExecutableJar file and i am getting error as "Class not Found. AND few files in that link are empty

I doubt am I using older version files. If I am using the older links, Kindly provide me the new link from which i can import Bio4j

Best

Pavan

[Pablo Pareja Tobes]

I Pavan,

Sorry for the delay but these past few days have been incredibly busy around here (we're applying for the Google Summer of Code as an organization with a set of proposals around Bio4j project and the deadline is on Friday! )

Fortunately this implies working on a much more complete and better organized documentation (as well as other exciting stuff) so if you're not in a rush for this I would suggest waiting a few days so that you can directly check the updated documentation next week ;)

Cheers,

Pablo

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Has recibido este mensaje porque estás suscrito al grupo "bio4j-user" de Grupos de Google.
Para anular la suscripción a este grupo y dejar de recibir sus correos electrónicos, envía un correo electrónico a bio4j-user+...@googlegroups.com.
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[Pablo Pareja Tobes]

I meant to write "Hi" not "I"... xD

Pablo

[Pavan Kumar]

Hello Pablo,

In addition to the execution jar files issues, 

I have another query regarding importing new databases to bio4j existing databases.

I want to import DrugBank and KEGG databases. So do i have to write cypher to make relationships between DrugBank and bio4j databases.

If not, what exactly i have to do to make my databases connected to the bio4j databases.