Location of blat, gfClient, gfServer and isPcr executables

[David da Silva Pires]

Hi, guys.

Is there any reason to keep the executables

blat

gfClient

gfServer

isPcr

inside the directory bin/blat instead of directly at bin directory?

Everytime I configure a GBiB or a GBiC and execute gbibaddtools or browserSetup.sh addTools, I have to remember to set up the PATH environment variable or make symbolic links at bin directory. At the same time, it seems that the scripts used to add kent utilities could put these files at bin directory without any problem. Just a suggestion...

Thanks for the great work by keeping the project alive.

Best regards.

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DAVID DA SILVA PIRES Especialista de Laboratório LABORATÓRIO DE CICLO CELULAR Tel: +55 11 2627-9734 www.butantan.gov.br

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[Matthew Speir]

Hi, David. 

Thank you for your question about downloading the blat utilities on GBiB and GBiC.

These blat utilities (blat, gfClient, gfServer, and isPcr) are separated from the rest as they have a different commercial license than the rest of the utilities. However, you make a great suggestion that after all of these utilities have been downloaded, that they can all exist in the same bin directory on GBiB/GBiC. I have made an internal work ticket to tweak those scripts so that after downloading the utilities are all in a single directory, but I can't give any estimate of when that will be implemented. 

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your suggestion.

We have made the changes to GBiB and the GBiC script to have the utilities in the bin directory.
The feature will be released next Tuesday (11/16). Thank you again for making your suggestion
on how to improve the GBiB and GBiC tools.

If you have any further questions, please reply to gen...@soe.ucsc.edu.

All messages sent to that address are archived on a publicly accessible Google Groups forum.

If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

Want to share the Browser with colleagues?

Host a workshop: https://bit.ly/ucscTraining

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CABJi3a%2B256yTww9AAV0OPkU0GV9cqH5JZpxCdM4S9n-EEiRSsw%40mail.gmail.com.