Dear Vanessa
Our IT staff is helping me install liftOver. He followed the instructions you provided and is still having a question below:
"I followed the directions here:
http://genome.ucsc.edu/admin/git.html
Which put everything in the "kent" directory in your home directory.
Now I'm following the README file in kent/src (I set MACHTYPE to x86_64).
Step 7 says "Go to the application you want to make and type make".
What application in kent/src has liftOver?"
Can you point me to the right directory?
Thanks
-Jianchao
-----Original Message-----
From: Vanessa Kirkup Swing [mailto:***@soe.ucsc.edu]
Sent: Thursday, December 09, 2010 1:15 PM
To: Yao, Jianchao
Cc: ***@soe.ucsc.edu; Pauline Fujita
Subject: Re: [Genome] liftOver - "command not found"
Dear Jianchao,
You can obtain the source tree by following the instructions provided here: http://genome.ucsc.edu/admin/git.html <http://genome.ucsc.edu/admin/git.html>
If you have further questions, please contact the mailing list.
Vanessa Kirkup Swing
UCSC Genome Bioinformatics Group
----- Original Message -----
From: "Jianchao Yao" <***@cshl.edu>
To: "Pauline Fujita" <***@soe.ucsc.edu>
Cc: ***@soe.ucsc.edu
Sent: Thursday, December 9, 2010 8:21:19 AM GMT -08:00 US/Canada Pacific
Subject: Re: [Genome] liftOver - "command not found"
Hi, Pauline
liftOver: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required
by liftOver)
Our IT just told me that
"GLIBC is a library which is an inherent part of the Linux kernel on all the HPCC nodes. It cannot be updated without a massive Linux upgrade of the entire cluster, which would break lots of installed software. That is not practical. Basically, we will need to upgrade by replacing the HPCC with a new system (we are trying to find funding).
This code was built/compiled for a newer Linux than the one we have, which is:
[***@blade169 ~]# uname -r
2.6.9-42.0.3.ELsmp"
They suggested me to get the source code for liftOver to use the GLIBC we have.
Could you help me on this? Thanks a lot!
-Jianchao
-----Original Message-----
From: Pauline Fujita [mailto:***@soe.ucsc.edu]
Sent: Wednesday, December 08, 2010 5:53 PM
To: Yao, Jianchao
Cc: ***@soe.ucsc.edu
Subject: Re: [Genome] liftOver - "command not found"
Hello Jianchao,
The error indicates that bash is not able to locate the liftOver program. You can either add the location of liftOver to your bash PATH environment variable, or you can specify the path when you run it. If you are in the directory where liftOver resides, type:
./liftOver
Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at ***@soe.ucsc.edu <mailto:***@soe.ucsc.edu> .
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu <http://genome.ucsc.edu>
I just downloaded liftOver for linux.x86_64 but after I typed liftOver
in the command line, I got
Ø -bash: liftOver: command not found
I tried liftOver for linux.i386 but still got the same error..
Can someone advise me on this error? Thanks in advance
-Jianchao
************************************
Jianchao Yao, Ph.D.
Woodbury Genome Center
Cold Spring Harbor Laboratory
500 Sunnyside Boulevard
Woodbury, NY 11797
************************************
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