[Gmod-help] Re: [Gmod-gbrowse] Help Installing Gmod-UCSC Plugin
Scott Cain
cain.cshl at gmail.com
Mon Dec 8 09:30:32 EST 2008
Hi Ramiro,
The file Gbrowse.conf doesn't make it debut until GBrowse 2.0 is
released, and I assume you are using 1.69 (or pre-1.70), so the
configuration parameters should go in the data source configuration
file. So if you are testing with the yeast dataset, for example, the
configuration would go in yeast.conf.
Scott
On Mon, Dec 8, 2008 at 7:33 AM, Ramiro Costa
<costar at childpsych.columbia.edu> wrote:
> Hi Angie,
>
> Again, thanks for the help, you Lincoln and other people from the
> mailing list have been very helpful.
>
> I've finally been able to compile Gbrowse with the UCSC plugin in it,
> now I'm trying to test the installation.
> I just have a question, I'm in the configuration section of "GBrowse
> UCSC Plugin Install HOWTO" and not sure where the configuration
> parameters should be placed. In the instructions it says it should be
> placed in the file datasource.conf, but that apparently was for an
> earlier version of Gbrowse, is this so?. Searching the web I found that
> that file in later versions changed to Gbrowse.conf, but can't find it
> either. I eventually found there's a plugin section in the configuration
> file for a given database (volvox.conf, for example), so I thought of
> including the configuration parameters there, is this correct?
> Anyway, I'm also concerned about how the [GENERAL] section of the
> database configuration file should be configured to use the UCSC plugin,
> do you have a sample file? Please let me know.
>
> Thanks again for your time and consideration.
>
> Ramiro
>
>>>> Angie Hinrichs <angie at soe.ucsc.edu> 11/26/08 3:34 PM >>>
> Hi Ramiro,
>
> Thanks for giving that a try, and sorry it's not compiling yet. I see
> a couple problems in the commands shown now:
>
> 1. It seems like the CCFLAGS are not propagating down all the way.
> The compile command that fails seems to have somewhat mangled flags:
> "-pipe -Wde-I/usr/include/gdbm" instead of
> "-pipe -I/usr/local/include".
>
> 2. It is not finding your MySQL client include file mysql.h:
>
> hdb.c:8:19: error: mysql.h: No such file or directory
>
> For #1, perhaps you could try setting CCFLAGS inside
> libucsc/libucsc/Makefile.PL instead of on the command line?
>
> For #2, locate the system directory that contains mysql.h and add that
> directory to @INC in libucsc/libucsc/Makefile.PL.
>
> Also, can you send the output of gcc -v? Here is what I get:
>
> Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
> --infodir=/usr/share/info --enable-shared --enable-threads=posix
> --disable-checking --with-system-zlib --enable-__cxa_atexit
> --disable-libunwind-exceptions --enable-java-awt=gtk
> --host=x86_64-redhat-linux
> Thread model: posix
> gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
>
> Thanks,
> Angie
>
>
> On Wed, 26 Nov 2008, Ramiro Costa wrote:
>
>> Hi All,
>>
>> First of all thanks a lot for your valuable help.
>>
>> Regarding the installation, I tried both passing the CCFLAGS parameter
>> in the Makefile.PL execution and also removing the -Werror from
>> libucsc/libucsc/Makefile.PL, but still no luck.
>> I still get the same error (see bellow), perhaps I'm making some
> mistake
>> in the installation process so I'm detailing the steps I'm following
>> bellow just to make sure these are correct:
>>
>> 1) I downloaded the latest Gbrowse version (1.69) and untarred it in a
>> temp dir
>> 2) I downloaded the Gmod UCSC plug files and untarred in a separate
> temp
>> dir
>> 3) I copied all non-CVS files from gmod-ucsc/Generic-Genome-Browser
> into
>> the corresponding locations in the GBrowse installation's
>> Generic-Genome-Browser tree
>> 4) I installed Gbrowse and got the errors bellow.
>>
>> Please let me know if I'm missing something in the above steps.
>>
>> Thanks again for the help!
>>
>> Regards,
>>
>> Ramiro Costa
>>
>>
> ====================================================================================
>> -bash-3.1$ pwd
>> /var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69
>> -bash-3.1$
>> -bash-3.1$ ls
>> bin cgi-bin conf DISCLAIMER GGB.def INSTALL lib
>> libucsc Makefile MANIFEST pm_to_blib README.berkeleydb
>> README.gff3 README.sessions t
>> blib Changes contrib docs htdocs install_util libalign
>> LICENSE Makefile.PL META.yml README README.fedora
>> README.MacOSX README.Ubuntu TODO
>> -bash-3.1$
>> -bash-3.1$ perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf
>> CGIBIN=/var> -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm'
>>
>> ----------------------------------------------
>> File Paths
>>
>> APACHE /usr/local/apache
>> CONF /etc/httpd/conf
>> HTDOCS /var/www/html
>> CGIBIN /var/www/cgi-bin
>> LIB
>> BIN
>> DO_XS 1
>> NONROOT
>> SELINUX
>>
>> (Run perl Makefile.PL -h for help on changing)
>> ----------------------------------------------
>> Writing Makefile for Bio::Graphics::Browser::CAlign
>> Warning: -L./libucsc changed to
>>
> -L/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/./libucsc
>> Note (probably harmless): No library found for -lucsc
>> Writing Makefile for Bio::Graphics::Browser::UcscTrackImage::libucsc
>> Writing Makefile for Bio::Graphics::Browser::UcscTrackImage
>> Writing Makefile for Generic-Genome-Browser
>> -bash-3.1$
>> -bash-3.1$
>> -bash-3.1$ make
>> make[1]: Entering directory
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
>> gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION=\"1.00\"
>> -DXS_VERSION=\"1.00\" -fPIC
>> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" CAlign.c
>> Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
>> chmod 644 CAlign.bs
>> rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
>> gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
>> -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
> CAlign.o
>> -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so \
>> \
>>
>> chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
>> cp CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
>> chmod 644 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
>> Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
>> make[1]: Leaving directory
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
>> make[1]: Entering directory
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
>> cd libucsc && make
>> make[2]: Entering directory
>>
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
>> gcc -c -I/usr/local/include -I/usr/include -I../inc -D_REENTRANT
>> -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wde-I/usr/include/gdbm -O2
> -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
>> -mtune=generic -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC
>> "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE" -DGBROWSE
>> -Wall hdb.c
>> hdb.c:8:19: error: mysql.h: No such file or directory
>> In file included from ../inc/hgColors.h:7,
>> from ../inc/hCommon.h:7,
>> from hdb.c:18:
>> ../inc/hvGfx.h: In function âhvGfxAdjXXâ:
>> ../inc/hvGfx.h:47: warning: ISO C90 forbids mixed declarations and
> code
>> hdb.c: In function âhTableOrSplitExistsDbâ:
>> hdb.c:988: warning: ISO C90 forbids mixed declarations and code
>> hdb.c: In function âfetchTwoBitSeqâ:
>> hdb.c:1086: warning: ISO C90 forbids mixed declarations and code
>> hdb.c: In function âseqGetâ:
>> hdb.c:1462: warning: ISO C90 forbids mixed declarations and code
>> hdb.c:1466: warning: ISO C90 forbids mixed declarations and code
>> hdb.c:1476: warning: ISO C90 forbids mixed declarations and code
>> hdb.c:1481: warning: ISO C90 forbids mixed declarations and code
>> hdb.c: In function âgetSeqAndIdâ:
>> hdb.c:1584: warning: ISO C90 forbids mixed declarations and code
>> hdb.c: In function âloadTrackDbâ:
>> hdb.c:3553: warning: ISO C90 forbids mixed declarations and code
>> hdb.c: In function âhTrackDbLoadSuperâ:
>> hdb.c:3833: warning: ISO C90 forbids mixed declarations and code
>> make[2]: *** [hdb.o] Error 1
>> make[2]: Leaving dire>
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
>> make[1]: *** [libucsc/libucsc.a] Error 2
>> make[1]: Leaving directory
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
>> make: *** [subdirs] Error 2
>> -bash-3.1$
>>
> ====================================================================================
>>
>>
>>
>>
>> >>> Angie Hinrichs <angie at soe.ucsc.edu> 11/25/08 4:38 PM >>>
>> Hi Lincoln and Ramiro,
>>
>> I agree with Dave that it is necessary to remove the
>> -Wdeclaration-after-statement from the compile command. The UCSC code
>
>> has many instances of variable declarations following statements. And
>
>> in case of other gotchas, it wouldn't hurt to also remove -Werror.
>>
>> I believe Makefile.PL gets some of its settings from the local perl
>> installation, i.e. if perl was compiled with those CCFLAGS, they
>> automatically are picked up by ExtUtils::MakeMaker. (Correct me if
>> I'm wrong, those with more MakeMaker experience.)
>>
>> Ramiro, here is something to try next: invoke Makefile.PL with a
>> trimmed-down CCFLAGS on the command line, like this (no linebreaks):
>>
>> perl Makefile.PL CCFLAGS='-D_REENTRANT -D_GNU_SOURCE
>> -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
>> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm'
>>
>> And you can modify libucsc/libucsc/Makefile.PL to remove the -Werror
>> if you like.
>>
>> If that doesn't work, please send the failing make output like you did
>
>> below.
>>
>> Thanks,
>> Angie
>>
>>
>> On Tue, 25 Nov 2008, Lincoln Stein wrote:
>>
>> > Hi Angie,
>> >
>> > Ramiro Costa is having problems with the UCSC plugin, and is
> probably
>> the
>> > first outsider to attempt this. Here is the original correspondence
>> and Dave
>> > Clement's analysis of the problem. Do you have any suggestions for a
>> fix?
>> >
>> > Lincoln
>> >
>> > On Tue, Nov 25, 2008 at 12:55 PM, Dave Clements, GMOD Help Desk <
>> > gmodhelp at googlemail.com> wrote:
>> >
>> > > Hi Ramiro,
>> > >
>> > > The problem appears to be that
>> > >
>> > > 1. The file axt.c contains a C variable declaration after a C
>> > > statement (not a problem in itself)
>> > > 2. The makefile specifically asks the C compiler for a warning
> when
>> > > that happens. (-Wdeclaration-after-statement)
>> > > 3. The makefile specifically asks for all warnings to be promoted
> to
>> > > fatal compile errors. (-Werror)
>> > >
>> > > However, I can't find anywhere in the Makefile.PL file for either
>> > > GBrowse or the UCSC plugin where they specifically ask for the
>> > > -Wdeclaration-after-statement or -Werror options on C
> compilations.
>> > >
>> > > Is it possible these options are coming from the local
> environment?
>> > > If you get rid of these 2 otpions it sh> > Does anyone with a
> better understanding of Makefile.PL have a
>> suggestion?
>> > >
>> > > Thanks,
>> > >
>> > > Dave C.
>> > >
>> > > Was this helpful? Let us know at
>> http://gmod.org/wiki/Help_Desk_Feedback
>> > >
>> > >
>> > > On Sat, Nov 22, 2008 at 4:55 AM, Ramiro Costa
>> > > <costar at childpsych.columbia.edu> wrote:
>> > > >
>> > > > Hi Lincoln,
>> > > >
>> > > > Thanks for your installation instructions. Here is what I get
> when
>> I try
>> > > > the installation (note the Warning line bellow):
>> > > >
>> > > > =======================================================
>> > > > perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf
>> > > > CGIBIN=/var/www/cgi-bin
>> > > >
>> > > > ----------------------------------------------
>> > > > File Paths
>> > > >
>> > > > APACHE /usr/local/apache
>> > > > CONF /etc/httpd/conf
>> > > > HTDOCS /var/www/html
>> > > > CGIBIN /var/www/cgi-bin
>> > > > LIB
>> > > > BIN
>> > > > DO_XS 1
>> > > > NONROOT
>> > > > SELINUX
>> > > >
>> > > > (Run perl Makefile.PL -h for help on changing)
>> > > > ----------------------------------------------
>> > > > Writing Makefile for Bio::Graphics::Browser::CAlign
>> > > > Warning: -L./libucsc changed to
>> > > >
>> > >
>>
> -L/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/./libucsc
>> > > > Note (probably harmless): > > > > Writing Makefile for Bio::Graphics::Browser::UcscTrackImage
>> > > > Writing Makefile for Generic-Genome-Browser
>> > > > =======================================================
>> > > >
>> > > > Then, when I try to proceed with the installation, I get the
>> following:
>> > > >
>> > > > =======================================================
>> > > > -bash-3.1$ make
>> > > > make[1]: Entering directory
>> > > >
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
>> > > > gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> > > > -Wdeclaration-after-statement -I/usr/local/include
>> -D_LARGEFILE_SOURCE
>> > > > -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
>> > > > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> > > > --param=ssp-buffer-size=4 -m64 -mtune=generic
> -DVERSION=\"1.00\"
>> > > > -DXS_VERSION=\"1.00\" -fPIC
>> > > > "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"
>> CAlign.c
>> > > > Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
>> > > > chmod 644 CAlign.bs
>> > > > rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
>> > > > gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>
>> -fexceptions
>> > > > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
>> CAlign.o
>> > > > -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
>
>> \
>> > > > \
>> > > >
>> > > > chmod 755
> ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
>> > > > cp CAlign.bs
>> ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
>> > > > chmod 644
> ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
>> > > > Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
>> > > > make[1]: Leaving directory
>> > > >
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
>> > > > make[1]: Entering directory
>> > > >
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
>> > > > cd libucsc && make
>> > > > make[2]: Entering directory
>> > > >
>> > >
>>
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
>> > > > gcc -c -I/usr/local/include -I/usr/include -I../inc
> -D_REENTRANT
>> > > > -D_GNU_SOURCE -fno-strict-aliasing -pipe
>> -Wdeclaration-after-statement
>> > > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
>> > > > -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
>> > > > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
>> > > > -mtune=generic -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC
>> > > > "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"
>> -DGBROWSE
>> > > > -Wall -Werror axt.c
>> > > > cc1: warnings being treated as errors
>> > > > axt.c: In function âaxtGetSubsetOnTâ:
>> > > > axt.c:358: warning: ISO C90 forbids mixed declara> >
>>
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
>> > > > make[1]: *** [libucsc/libucsc.a] Error 2
>> > > > make[1]: Leaving directory
>> > > >
>> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
>> > > > make: *** [subdirs] Error 2
>> > > > =======================================================
>> > > >
>> > > >
>> > > > Do you know why could this be.
>> > > >
>> > > > Thanks a lot!!
>> > > >
>> > > > Regards,
>> > > > Ramiro
>> > > >
>> > > > >>> "Lincoln Stein" <lincoln.stein at gmail.com> 11/12/08 1:39 PM
>>>>
>> > > > Hi Ramiro,
>> > > > The instructions assume that you have downloaded and unpacked
>> GBrowse
>> > > > into
>> > > > your home directory and have not yet installed it. Go to
>> www.gmod.org,
>> > > > download the tar file for the 1.69 release:
>> > > >
>> > > > http://sourceforge.net/project/showfiles.php?group_idUnpack it
>> into your
>> > > home directory, and then proceed from there. Not
>> > > > many
>> > > > people have tried the UCSC plugin install, so please let me know
>> what
>> > > > your
>> > > > experience is!
>> > > >
>> > > > Lincoln
>> > > >
>> > > > On Wed, Nov 12, 2008 at 10:20 AM, Ramiro Costa <
>> > > > costar at childpsych.columbia.edu> wrote:
>> > > UCSC
>> > > > tracks
>> > > > > into Gbrowse.
>> > > > >
>> > > > > I followed the instructions given in the tutorial (
>> > > > > http://gmod.org/wiki/GBrowse_UCSC_Plugin_Install_HOWTO) but
>> still not
>> > > > > clear to me.
>> > > > > I downloaded the plugin but got stuck at the installing step.
>> The
>> > > > tutorial
>> > > > > says I should copy all non-CVS files from
>> > > > gmod-ucsc/Generic-Genome-Browser/
>> > > > > into the corresponding locations in my GBrowse installation's
>> > > > > Generic-Genome-Browser tree. When I search for the
>> > > > Generic-Genome-Browser
>> > > > > tree, I only found an empty dir except for a hidden file named
>> > > > ".packlist".
>> > > > > The location of this dir is the following:
>> > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>>
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Generic-Genome-Browser
>> > > > >
>> > > > > Is this the correct place to install the plugin? Would someone
>> please
>> > > > > elaborate on the plugin installation steps?
>> > > > >
>> > > > > Thanks in advance!
>> > > > >
>> > > > > Regards,
>> > > > >
>> > > > > Ramiro
>> > > > >
>> > > > >
>> > > > >
>> > > >
>>
> -------------------------------------------------------------------------
>> > > > > This SF.Net email is sponsored by the Moblin Your Move
>> Developer's
>> > > > > challenge
>> > > > > Build the coolest Linux based applications with Moblin SDK &
> win
>> great
>> > > > > prizes
>> > > > > Grand prize is a trip for two to an Open Source event anywhere
>> in the
>> > > > world
>> > > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > > > > _______________________________________________
>> > > > > Gmod-gbrowse mailing list
>> > > > > Gmod-gbrowse at lists.sourceforge.net
>> > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > > > >
>> > > >
>> > > >
>> > > >
>> > > > --
>> > > > Lincoln D. Stein
>> > > >
>> > > > Ontario Institute for Cancer Research
>> > > > 101 College St., Suite 800
>> > > > Toronto, ON, Canada M5G0A3
>> > > > 416 673-8514
>> > > > Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
>> > > >
>> > > > Cold Spring Harbor Laboratory
>> > > > 1 Bungtown Road
>> > > > Cold Spring Harbor, NY 11724 USA
>> > > > (516) 367-8380
>> > > > Assistant: Sandra Michelsen <michelse at cshl.edu>
>> > > >
>> > > >
>> > > >
>>
> -------------------------------------------------------------------------
>> > > > This SF.Net email is sponsored by the Moblin Your Move
> Developer's
>> > > challenge
>> > > > Build the coolest Linux based applications with Moblin SDK & win
>> great
>> > > prizes
>> > > > Grand prize is a trip for two to an Open Source event anywhere
> in
>> the
>> > > world
>> > > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > > > _______________________________________________
>> > > > Gmod-gbrowse mailing list
>> > > > Gmod-gbrowse at lists.sourceforge.net
>> > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>> > >
>> >
>> >
>> >
>> Software Developer, UCSC CBSE / Genome Bioinformatics Group
>>
>
> --
> angie at soe.ucsc.edu
> Software Developer, UCSC CBSE / Genome Bioinformatics Group
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
More information about the Gmod-help
mailing list