Index of /admin/exe/linux.x86_64

[周泽(Ze Zhou)]

Dear professor,

        I am doing a research about mental disease. And I have 2 problem about file gc5base.wib.

        

        Firstly, I downloaded software hgWiggle from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ , but when I run the hgWiggle, it always tell me cannot find file like this."

drwxr-xr-x  2 zhouze zhouze      4096  9  8 14:36 ./

drwxr-xr-x 21 zhouze zhouze      4096  9  9 15:24 ../
-rw-------  1 zhouze zhouze   9869820  9  8 13:51 gc5Base.txt
-rw-------  1 zhouze zhouze 579466605  8 28 16:04 gc5Base.wib
lrwxrwxrwx  1 zhouze zhouze        11  9  8 13:54 gc5Base.wig -> gc5Base.txt
-rwxrwxrwx  1 zhouze zhouze  13121090  9  8 13:52 hgWiggle*
zhouze@zhouze:~/wig$ ./hgWiggle -doBed gc5Base
No such file or directory

mustOpenFd: Can't open /gbdb/gasAcu1/wib/gc5Base.wib to read".

        

        Secondly I download kent and fellow the direction of http://permalink.gmane.org/gmane.science.biology.ucscgenome.general/6377. and when I use the commend "make" in dirctory ./kent/src/lib, although I have already install openssl correctlly, it always tells me that

 "udc.c:39:25: fatal error: openssl/sha.h: No such file or directory 

 #include <openssl/sha.h>
compilation terminated.

make: *** [udc.o] error 1".

        

        I have no idea about how to dealing with it . And I am very greatful if you can help me.

Yours,

Sincerely

---

周泽(Ze Zhou)

BGI Shenzhen  Research

[Jonathan Casper]

Hello Ze Zhou,

Thank you for your question about using the hgWiggle and gc5Base.wib files. I suspect the problem here is that hgWiggle starts by reading the gc5Base.wig file, and entries in that file are telling it to look in the wrong place for gc5Base.wib. Your gc5Base.wig file most likely includes file locations like "/gbdb/gasAcu1/wib/gc5Base.wib". That path doesn't exist on your system, so hgWiggle complains because it can't find that file. The solution is to edit your gc5Base.wig file and replace all instances of "/gbdb/gasAcu1/wib/gc5Base.wib" with "gc5Base.wib". That will tell hgWiggle that the gc5Base.wib file is contained in the current directory. Alternatively, you can replace the "/gbdb" path with the full path to gc5Base.wib in your file system.

The instructions in the mailing list question that you reference are close to 5 years old. If you would like to just download source for the command line tools, we suggest that you obtain our userApps source package from http://hgdownload.soe.ucsc.edu/admin/exe. The userApps.src.tgz file expands to contain source code to compile our tools along with some scripts that make the process much more simple. If you would really like to compile tools directly from the kent source tree, then you can find more detailed instructions within the kent tree in the file src/product/README.building.source. The error you report suggests that there is a missing library in your OpenSSL installation - the file "sha.h" is missing. This might be due simply to a version difference between the OpenSSL package you installed and the one currently in use at UCSC. Alternatively, the sha.h library files may not have been installed so that the compiler knows where to find them. You could try checking your /usr/include/ directory to see if sha.h is present there. In the worst case, you can turn off USE_SSL in the browser compile scrips to avoid this problem altogether. Instructions for doing this can also be found in the README.building.source file.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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