Compiling problems with Kent

[neophte]

Hi,

I am trying to use some tools from kent src, particularly the twobit2fa to convert the hg19.2bit file to fasta.

In the past, when I've tried to work with Kent, I always get some kind of error and have been able to circumvent it somehow. This time I am trying to compile twobit2fa and I am getting this error message:

gcc -O -g -Wall -Wno-unused-variable -o /Users/kizeeetienne/bin//twoBitToFa twoBitToFa.o ../../lib//jkweb.a -pthread -lssl -lcrypto -lpng -lm
i686-apple-darwin11-llvm-gcc-4.2: ../../lib//jkweb.a: No such file or directory
make: *** [twoBitToFa] Error 1

Could some pls explain what this means; I am new to Bioinfo and have no idea what to do with this error. Something tells me that it is a compatibility issue with mac osx and kent but I have no idea how to fix it???

I would love to get rid of this problem with Kent once and for all before it comes back to haunt me for the third and fourth times.

Thanks

[Pirol]

Hi @ all,

I have huge problems to install some modules of Kent source tree (e.g. lavToPsl or pslSwap).
So far, I could install all stuff and changed also all variables (MACHTYPE, USE_XXX, ...). Furthermore, I installed samtools new and added tabix. After that, I tried to copy samtools libbam.a to every lib-folder I have (and I changed also the PATH-variables) and so on. I tried everything I know but I receive always this message:

gcc -O -g -o .../x86_64/pslSwap pslSwap.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lm -pthread -lssl -lcrypto /opt/local/lib/libpng.a /libbam.a /libtabix.a -lz -lm
i686-apple-darwin11-llvm-gcc-4.2: /libbam.a: No such file or directory
i686-apple-darwin11-llvm-gcc-4.2: /libtabix.a: No such file or directory
make: *** [.../x86_64/pslSwap] Error 1

Does anyone of you know what I could do? I would be verry happy about every help I could receive!

Thanks!

[GenoMax]

Why is gcc thinking that "libbam.a" is in the "/" (root) directory? What exactly are you compiling? (I think you may only need to provide the option "-lbam" not the full file name).

Are you not able to use the pre-compiled executables available here: http://hgdownload.cse.ucsc.edu/admin/exe/?

[Pirol]

Hi GenoMax,

thank you very much for your comments!
Finally, I used the pre-compiled executables. Thanks for the memory... I forget them totally

But nevertheless, I really don't know why there is this installation problem. I don't know why gcc thinks that "libbam.a" is in the root directory. I followed only the instructions of the README-file and after typing "make" this was the result.

[Macspider]

Hi GenoMax,

thank you very much for your comments!
Finally, I used the pre-compiled executables. Thanks for the memory... I forget them totally

But nevertheless, I really don't know why there is this installation problem. I don't know why gcc thinks that "libbam.a" is in the root directory. I followed only the instructions of the README-file and after typing "make" this was the result.

Hi,
I know it's been a while, but may I ask you which are the precompiled files you used? I'm having similar problems and I can't get out of this. Please, if you remember, could you post me some links?

Thank you!

[Pirol]

Unfortunately, I cannot remember which precompiled files I used and I cannot check them anymore...
But nevertheless, the version you need depends on your kernel.
Here is some help to find out (if you're using Mac OS X):

http://apple.stackexchange.com/questions/12666/how-to-check-whether-my-intel-based-mac-is-32-bit-or-64-bit

[Macspider]

Unfortunately, I cannot remember which precompiled files I used and I cannot check them anymore...
But nevertheless, the version you need depends on your kernel.
Here is some help to find out (if you're using Mac OS X):
http://apple.stackexchange.com/quest...-bit-or-64-bit

Thank you. Hope it helps.