bigfile install error

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bigfile install error

JINGJING JIN-2
Dear all,

Before I install Bio-Bigfile in the server, I try to install the kent tree library.

However, according to the instruction in the  src/product/REAME.building.source, there are some strange errors like this:

[ns_10@yejianlab stringify]$ make
gcc -O -g -o /home/ns_phd10/bin/x86_64/stringify stringify.o    ../../lib/x86_64/jkweb.a -rdynamic -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -lssl -lcrypto -lstdc++ -lrt -lm  -pthread -lpng -lm -lm
/usr/bin/ld: cannot find -lmysqlclient
collect2: ld returned 1 exit status
make: *** [/home/ns_phd10/bin/x86_64/stringify] Error 1


It seems the mysqlclient library is missing, however, I have already install the mysql library in my server:

[root@tll-yejianlab ~]# yum install mysql mysql-server
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
Setting up Install Process
Package mysql-5.1.71-1.el6.x86_64 already installed and latest version
Package mysql-server-5.1.71-1.el6.x86_64 already installed and latest version
Nothing to do


Can anyone give me some suggestion about how to install this library?

Thanks!

Jingjing



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Re: bigfile install error

Scott Cain
Hi Jingjing,

I did the same thing the first time I tried to build the Kent libraries.  You don't need to make everything in the source tree, only lib directory.  These are the directions from the BigFile README:

Step 1) COMPILE JIM KENT SOURCE TREE

To compile this module, you must first download, unpack and compile
the Jim Kent source tree, located at
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip. The commands needed to
get, unpack and compile the necessary file are:

 wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
 unzip jksrc.zip
 cd kent/src/lib
 export    MACHTYPE=i686    # for a 64-bit system
 # export  MACHTYPE=i386    # for a 32-bit system
 make
 cd ..
 export KENT_SRC=`pwd`

Let us know if that doesn't work for you.
Scott



On Tue, Dec 3, 2013 at 1:10 AM, JINGJING JIN <[hidden email]> wrote:
Dear all,

Before I install Bio-Bigfile in the server, I try to install the kent tree library.

However, according to the instruction in the  src/product/REAME.building.source, there are some strange errors like this:

[ns_10@yejianlab stringify]$ make
gcc -O -g -o /home/ns_phd10/bin/x86_64/stringify stringify.o    ../../lib/x86_64/jkweb.a -rdynamic -L/usr/lib64/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -lssl -lcrypto -lstdc++ -lrt -lm  -pthread -lpng -lm -lm
/usr/bin/ld: cannot find -lmysqlclient
collect2: ld returned 1 exit status
make: *** [/home/ns_phd10/bin/x86_64/stringify] Error 1


It seems the mysqlclient library is missing, however, I have already install the mysql library in my server:

[root@tll-yejianlab ~]# yum install mysql mysql-server
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
Setting up Install Process
Package mysql-5.1.71-1.el6.x86_64 already installed and latest version
Package mysql-server-5.1.71-1.el6.x86_64 already installed and latest version
Nothing to do


Can anyone give me some suggestion about how to install this library?

Thanks!

Jingjing



------------------------------------------------------------------------------
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organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk
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