Hi Galt, Maybe I should ask a more basic question before I keep working on this config. I've heard it can take weeks to set up the genome browser, so let me make sure I need it for my purposes.
Our lab does many chip-based studies on human and mouse genome. So I need the basic browser, and I need the human and mouse datasets. Should I use the full browser install or get the minimal browser and then install the species-specific sets? Re: mysqlclient --- I have the .a file and it is in /usr/libs/ I also have the mysql headers, and they are in /usr/include/mysql So I do have the files. The Debian install in Ubuntu said something about needing a "shared" library and had the MYSQLLIBS variable set up to point to "-lmysqlclient -lz". I've tried this (again, with no success) but a) do I need do set this var this way or the other way (libmysqlclient.a)? b) Is that variable set correctly in the example? (There is another bug in the example: it says to go to src/libs (which doesn't exist) and type "make compile $DIRS" which only returns a statement saying there is no target "compile" for make.) Thanks,S -----Original Message----- From: Galt Barber [mailto:[email protected]] Sent: Thu 3/4/2010 1:17 PM To: Shraddha Pai Cc: [email protected] Subject: Re: [Genome] Source code compile failing Do you have the mysql client libs installed? These are required. It has nothing to do with firewall. In other words, the paths your are giving in $MYSQLLIBS and $MYSQLINC need to point to real things at exist on your system. The only minor thing is that with MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz" we have tacked on the -lz for the zlib dependency. -Galt ----- Original Message ----- From: "Shraddha Pai" <[email protected]> To: "Galt Barber" <[email protected]> Cc: [email protected] Sent: Wednesday, March 3, 2010 6:25:53 PM GMT -08:00 US/Canada Pacific Subject: RE: [Genome] Source code compile failing Hi Galt, That fixed the hgSuggest.c error - thanks! I now have another problem. When I type the "make install" command, I am told that MYSQLLIBS and MYSQLINC is not defined, whereas you can see from the "echo" command that it is. >>> p...@paitemp:/usr/local/kent/src/hg# sudo make install DESTDIR=/mydisk2/UCSC CGI_BIN=/mydisk2/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 p...@paitemp:/usr/local/kent/src/hg# echo $MYSQLLIBS /usr/lib -lmysqlclient -lz p...@paitemp:/usr/local/kent/src/hg# echo $MYSQLINC /usr/include/mysql r...@paitemp:/usr/local/kent/src/hg# <<< I get the same error if MYSQLLIBS = "/usr/lib/libmysqlclient.a -lz" or MYSQLLIBS = "-lmysqlclient -lz" ---> this param was suggested in the Debian/Ubuntu build script here ( http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntu ). I'm not sure if the shared library option is necessary in my case because I plan to install it on a machine internal to a firewall. Thanks again, Shraddha -----Original Message----- From: Galt Barber [ mailto:[email protected] ] Sent: Wed 3/3/2010 6:56 PM To: Shraddha Pai Cc: [email protected] Subject: Re: [Genome] Source code compile failing Please patch src/hg/hgSuggest/hgSuggest.c as follows: retrieving revision 1.2 diff -r1.2 hgSuggest.c 74c74 < safef(previous, sizeof(previous), row[0]); --- > safef(previous, sizeof(previous), "%s", row[0]); We have patched our main branch but it will take a while to hit the public release (a few days to a couple of weeks). -Galt Shraddha Pai wrote: > Hi all, > I'd like to install a local copy of the genome browser. > I'm following instructions from here: > http://genome.ucsc.edu/admin/jk-install.html > > When I try to type "make compile" or "make $DIRS" (from the Debian > instructions here: > http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubunt > u), I get the following error: > > ( cd hgSuggest && echo hgSuggest && make compile) > hgSuggest > make[1]: Entering directory `/usr/local/kent/src/hg/hgSuggest' > gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized > -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 > -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc > -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o > hgSuggest.o -c hgSuggest.c > cc1: warnings being treated as errors > hgSuggest.c: In function รข: > hgSuggest.c:74: error: format not a string literal and no format arguments > make[1]: *** [hgSuggest.o] Error 1 > make[1]: Leaving directory `/usr/local/kent/src/hg/hgSuggest' > make: *** [hgSuggest.compile] Error 2 > r...@paitemp:/usr/local/kent/src/hg# > <<< > > What am I doing wrong? > - I've created ~/bin/x86_64 (my $MACHTYPE) > - Here are my environment variables: >> echo $MYSQLLIBS > -lmysqlclient -lz >> echo $MYSQLINC > /usr/include/mysql >> echo $MACHTYPE > x86_64 >> echo $DIRS > SCRIPTS=/usr/local/bin CGI_BIN=/usr/lib/cgi-bin DOCUMENTROOT=/var/www/genome > BINDIR=/usr/local/bin ENCODE_PIPELINE_BIN=/usr/local/bin > > Other info: > - My machine runs Ubuntu 9.10. > - I've installed mysql-client mysql-server libmysqlclient-dev and apache2 > > Is there a binary for Ubuntu that I can just download and use? > > Thanks so much, > Shraddha > > ------------------------------------------------------ > Shraddha Pai > Postdoctoral fellow, Petronis lab > The Krembil Family Epigenetics Research Laboratory > Centre for Addiction and Mental Health > 250 College Street, Toronto, ON. > > > > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
