GBrowse not recognizing the kent source tree

[Macspider]

Hi all,

When I'm installing GBrowse I'm experiencing some problems. When it comes to the point of running ./Build installdeps to fix the dependencies that are lacking, one of these is Bio:B::File. When trying to install it, it asks me to provide the path to the kent source tree. When I do, it doesn't find that it needs to find in there, which are two files, jkweb.a and bigWig.h.

This is the complete output:

root@{machine}:/../GBrowse# ./Build installdeps 
Checking optional dependencies:
GBrowse installer [Install DB_File::Lock?] n
GBrowse installer [Install Bio::DB::BigFile?] y
Reading '/root/.cpan/Metadata'
  Database was generated on Mon, 11 Jul 2016 09:17:02 GMT
Running install for module 'Bio::DB::BigFile'
Checksum for /root/.cpan/sources/authors/id/L/LD/LDS/Bio-BigFile-1.07.tar.gz ok
Configuring L/LD/LDS/Bio-BigFile-1.07.tar.gz with Build.PL

This module requires the compiled jkweb.a library from Jim Kent's source tree.
If you haven't already done so, please download the source from
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, unpack it, and build the
contents of the "kent/src/lib" subdirectory as directed in the README. Then
enter the location of the "kent/src" subdirectory at the prompt below. To prevent
this message from appearing in the future, set the environment variable KENT_SRC 
to point to the "kent/src" subdirectory.

Please enter the location of Kent source tree: /home/schmat/programs/kentUtils/src

Can't find the bigWig.h and jkweb.a files at this location.

I already tried exporting the $KENT_SRC variable, it doesn't work. Moreover, if you search the two files through the shell command "find" you will find them.

root@{machine}:/../kentUtils/src# find . -name bigWig.h && find . -name jkweb.a 
./inc/bigWig.h
./lib/local/jkweb.a

Has anybody encountered this problem so far? Please help, I really need a solution to this. Thank you very much in advance!

[Richard Finney]

Just a guess.

Put a slash "/" after the "src"

[Macspider]

Just a guess.

Put a slash "/" after the "src"

We literally tried every combination in that sense.

[GenoMax]

Tried to copy both of those files into /path_to/kent/src/lib ?

[Macspider]

Tried to copy both of those files into /path_to/kent/src/lib ?

Yep. Other errors rise, they need to be where they are!

EDIT:
It doesn't show different errors, it keeps showing the same one.

[GenoMax]

Yep. Other errors rise, they need to be where they are!

Just to confirm. You made a copy and not a move so there were copies in both places? What other errors arise?

[Macspider]

Just to confirm. You made a copy and not a move so there were copies in both places? What other errors arise?

Yes that was a copy, even though I tried with both move and copy. There is no particular error, but the installation program keeps saying that it can't find those files in that directory. I checked again and it wasn't letting other errors arise, rather keeping showing the same error. I will edit the post above.

[GenoMax]

Did you compile these using sudo? I am not sure if the solution in this thread is applicable but check it out just in case: https://sourceforge.net/p/gmod/mailm...sage/26342612/

[Macspider]

I did everything as super user and already followed that exact thread on sourceforge that you sent me, making with -fPIC and exporting the MACHTYPE variable everytime. I think it might be something related to how these files that i lack are compiled, maybe they don't arise any error but are somehow corrupted inside without raising errors or warnings (although strange...)

[geocarvalho]

Someone solved this? I have the same problem using kentUtils

[Macspider]

Someone solved this? I have the same problem using kentUtils

Yes, I solved it in the end. Unluckily for you, there isn't a clear reason why it worked in the end, but it did. How I did it:

1 - went to the root directory (/)

2 - downloaded the jksrc.zip file there (not the github one, but the old one) here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

3 - compiled it following the instructions in its readme (some libs have to be compiled first, especially using -fPIC)

make CXXFLAGS=-fPIC CFLAGS=-fPIC CPPFLAGS=-fPIC

4 - installed GBrowse using default settings which, for whatever reason, in the root directory recognize the kent source tree.

NOTE 1:
Always make sure that your machine type ($MACHTYPE) is what you get with uname -p (processor). If you check uname -m (machine type) you might have something like x86_64-linux but you need to have something simple like x86_64 only.
To change it just:

MACHTYPE="x86_64"
echo $MACHTYPE

NOTE 2:
Use samtools version 0.1.19 and not newer versions, the newer ones are not compatible with that kent source tree and depending on the github release you have you get different samtools compatibility issues. 0.1.19 and jksrc.zip together work.

https://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2/download

NOTE 3:
Be aware of the existence of JBROWSE, easier to install and to use, which only lacks the image export function but can be wrapped using other tools which you will easily find googling.

http://jbrowse.org/jbrowse-1-12-1/

It took me around 2.7% of my PhD to figure out all of this. Good luck!