HELP: hgLoadSqlTab make error

[Zhibo Ma]

Hi,

I have installed a minimum UCSC genome browser on my laptop using your automated GBiC script. It worked fine with mirroring a selected genome.

But I want to add a new genome assembly. So I followed the the instructions from this genomewiki site:  http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database

Everything went smoothly till step 8:

8. Load the chromInfo table:

   $ hgLoadSqlTab abcDef1 chromInfo $HOME/kent/src/hg/lib/chromInfo.sql \

             bed/chromInfo/chromInfo.tab

 

hgLoadSqlTab executable has to be compiled from the kentUtil tree. I think I have the most recent source code which I git cloned from this site:

git://genome-source.soe.ucsc.edu/kent.git.

However, when I run the make from kent/src/hg/makeDb/hgLoadSqlTab/     an error occurred:

Make: *** No rule to make target ‘../../../lib/x86_64/jkh.gap.a’ , need by ‘/home/mzhibo/bin/x86_64/hgLoadSqlTab’ . Stop

 

The makefile looks like this:

   1 include ../../../inc/common.mk

   2

   3 L += $(MYSQLLIBS) -lm

   4 MYLIBDIR = ../../../lib/$(MACHTYPE)

   5 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a

   6

   7 O = hgLoadSqlTab.o

   8

   9 hgLoadSqlTab: $O $(MYLIBS)

  10         ${CC} ${COPT} ${CFLAGS} -o ${BINDIR}/hgLoadSqlTab $O $(MYLIBS) $L

  11         ${STRIP} ${BINDIR}/hgLoadSqlTab${EXE}

  12

  13 clean::

  14         rm -f ${O}

 

So I checked the “../../../lib/x86_64/ “ directory, there is only one spaceHoder.c file. I check some other repository for kentUtils on github, none of them includes jkhgap.a and jkweb.a files.

 

Do you know how to compile this tool without those two .a lib files, or how to get those two files?

Really appreciate!

Zhibo

 

 

 

 

Zhibo Ma

Graduate student

Department of Cellular Biology

University of Georgia

Athens, GA 30605

 

[Zhibo Ma]

The system is ubuntu 16.04.4 LTS.

I read more about the kent tree and found that these two libraries need to be made on my own computer from the kent/src/ by running make libs

I was able to get the jkhgap.a library from kent/src/hg/lib. However, when I try to make the jkweb.a library from the kent/src/lib, it throws me an error:

gcc -O -g  -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64   -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../htslib -I/include -I/usr/include/libpng12  -o uuid.o -c uuid.c
In file included from uuid.c:9:0:
../inc/uuid.h:8:23: fatal error: uuid/uuid.h: No such file or directory
compilation terminated.
../inc/common.mk:371: recipe for target 'uuid.o' failed
make: *** [uuid.o] Error 1

After some more research, it seems to be a issue with uuid library. 

I installed uuid and uuid-dev (not sure exactly which one really helped) by running sudo apt-get install uuid uuid-dev. Then I was able to successfully build all the libs from the kent/scr/.

Hopefully this would be helpful to other beginners like me..

Zhibo

[Matthew Speir]

Hi Zhibo,

Thank you for your questions about building some of the UCSC Genome Browser utilities. I'm glad that you were able to resolve the issue.

If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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