how to use the file-conversion utilities?

[peikai]

Dear all,

 

I am trying to convert bigBed files to Bed files.

 

For this purpose, I am trying the ‘stand-alone’ utilities listed at:

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

I suppose I can download any of this file to a local directory, and use

chmod +x to make the file executable. I did try so, but found it does not work.

 

Particularly, I downloaded the utility “bigBedToBed” to a local directory (say dir1).

I then performed the following:

chmod +x bigBedToBed

./ bigBedToBed

But I got the message:

Bash: ./ bigBedToBed: cannot execute binary file

 

I tried this on cygWin, and on a ubuntu Linux running on VM-Ware.

(My actual OS is Win7-64bit. The VMware is running on Win7.

And the Ubuntu is running on the VMware)

 

Can anyone tell me how to install the utility “bigBedToBed”?

 

Thanks

 

P Chen

 

 

 

[Hiram Clawson]

Try the command on the Ubuntu system without the blank
between the ./ and the bigBedToBed command:

$ ./bigBedToBed

[peikai]

Dear Hiram,

Thank you for your help.

But it does not appear to work out.
Here is what I got when I followed your suggestion:
pchen@pchen:~/Downloads$ ll big*
-rwxrwxr-x 1 pchen pchen 334448 2012-09-10 13:02 bigBedToBed*
pchen@pchen:~/Downloads$ ./bigBedToBed
bash: ./bigBedToBed: cannot execute binary file

Would somebody else also suggest to me on how to use the 'standalone'
format-conversion utilities on UCSC?

Thanks a lot

Best
PChen

[Hiram Clawson]

Evidently your Ubuntu under VMWare is too much different
than the environment under which the utilities were built.

You can use the table browser at the UCSC genome WEB site
to download the bigBed table as a bed file.

--Hiram

[peikai]

Dear Hiram,

Thanks a lot.

What amazes me is that there are no windows-based versions of the utilities.

I am downloading a large number of bigbed files (from ENCODE).
It is a big headache to read these files (into R), with a standardized tool.
(I can write some C/C++ codes to read the binary files, based on the
reported structure.
But it is kinda not standardized and not guaranteed with quality. So I am
looking for
some tools that do the job.)

Perhaps let me try ubuntu-on-the-USB-stick (i.e., without a VMware) to do
the job.

Meanwhile, I am interested to learn if there is any way that can convert
these files in
batch in windows.

Appreciate your help.

PChen

-----Original Message-----
From: Hiram Clawson [mailto:hi...@soe.ucsc.edu]
Sent: Wednesday, September 12, 2012 11:40 AM
To: peikai
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] how to use the file-conversion utilities?

[peikai]

Dear Hiram,

I have finally figured out a way to use these utilities: by installing
a 64-bit ubuntu on VMware.

Although I am enjoying these free software, I need to say one word about
UCSC utilities:
it is quite amazing to see that only linux-64-bit and MAC32/64 versions of
the utilities are available; whereas Windows 32/64-bit and linux
32-bit---supposedly the most popular platforms---are almost (except one
among tens of others for lin32) completely not available.
(I don't really see the difficulty to re-compile the codes for a different
OS)

(I hope I am wrong in that they do have Windows-based utilities.)

But, certainly, thanks a lot for your help; and for UCSC's software.


Best
Peikai

-----Original Message-----
From: Hiram Clawson [mailto:hi...@soe.ucsc.edu]

Sent: Wednesday, September 12, 2012 11:40 AM

To: peikai
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] how to use the file-conversion utilities?