Your sudo command makes your commands run under the root identity
which does not have your shell settings.
Please note, your installation needs to have these directories
right next to each other in one location:
./htdocs/
./cgi-bin/
./trash/
If you want to use /usr/lib/cgi-bin/
your will also need Apache document root as:
/usr/lib/htdocs/
and trash in: /usr/lib/trash/
To enable writing to these directories, run a sudo:
$ sudo chmod 777 /usr/lib/cgi-bin /usr/lib/htdocs /usr/lib/trash
Then your make install DESTDIR=/usr/lib CGI_BIN=/cgi-bin
will write to /usr/lib/cgi-bin
--Hiram
----- Original Message -----
From: "Minh Bui" <[email protected]>
To: [email protected]
Sent: Friday, August 27, 2010 6:21:56 AM GMT -08:00 US/Canada Pacific
Subject: [Genome] Error when Installing UCSC Genome Browsers
Hi everyone,
I am trying to install UCSC Genome Browser on my local computer (Ubuntu
10.04)
I follow this instruction:
http://genome.ucsc.edu/admin/jk-install.htmluntil Step 7
and I get this error.
m...@minh-desktop:~$ echo $MACHTYPE
i686
m...@minh-desktop:~$ echo $MYSQLLIBS
/usr/lib/libmysqlclient.a -lz
m...@minh-desktop:~/Downloads/jksrc/src/hg$ echo $MYSQLINC
/usr/include/mysql
m...@minh-desktop:~$ cd kent/src/hg
bash: cd: kent/src/hg: No such file or directory
m...@minh-desktop:~$ cd '/home/minh/Downloads/jksrc/src/hg'
m...@minh-desktop:~/Downloads/jksrc/src/hg$ sudo make install
DESTDIR=/usr/lib CGI_BIN=/cgi-bin/ucsc
ERROR: missing MYSQLLIBS or MYSQLINC definitions in environment
these are typically,
for bash shell users:
$ export MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz"
$ export MYSQLINC=/usr/include/mysql
for csh/tcsh shell users:
% setenv MYSQLLIBS "/usr/lib/mysql/libmysqlclient.a -lz"
% setenv MYSQLINC /usr/include/mysql
See also: http://genome.ucsc.edu/admin/jk-install.html
make: *** [hgLib] Error 255
Why does it say MYSQLLIBS and MYSQLINC are missing? I do have them when I
echo them...
By the way, when the instruction says make install
DESTDIR=/destination/prefix CGI_BIN=/cgi-bin/path.
What does it mean "/destination/prefix"? My cgi-bin folder is in
/usr/lib/cgi-bin. Does it mean DESTDIR= /usr/lib and CGI_BIN = /cgi-bin??
Please help,
Thank you,
Minh.
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
