Hello Hiram, That works. thank you so much. Sorry I require so much hand holding with this.
I have another question. When I try to load a BED file into the custom tracks I get the following error: [r...@franknstein ~]# hgLoadBed rheMac2 bedrheMacExample Abhishek-bfast.reported.file.080513_HWI-EAS172_20DYG.l7.Mac2MacCombo.2MM.k18w19.v2.2.bed Reading Abhishek-bfast.reported.file.080513_HWI-EAS172_20DYG.l7.Mac2MacCombo.2MM.k18w19.v2.2.bed Loaded 3688697 elements of size 4 Sorted Creating table definition for bedrheMacExample Can't start query: CREATE TABLE bedrheMacExample ( bin smallint unsigned not null, chrom varchar(255) not null, chromStart int unsigned not null, chromEnd int unsigned not null, name varchar(255) not null, #Indices INDEX(name(16)), INDEX(chrom(5),bin) ) mySQL error 1005: Can't create table 'bedrheMacExample' (errno: 13) I checked the forums and it seems to be an issue with some database cleaning script on the genome browser. However, there wasn't any solution mentioned. Abhishek Goel Staff Research Associate Geschwind Laboratory, UCLA Neurology Gonda Neuroscience and Genetics Research Center #2309 University of California Los Angeles 695 Charles E. Young Dr. South Los Angeles, CA 90095 Tel: (310) 794-7537 Fax: (310) 267-2401 On Tue, Nov 10, 2009 at 9:55 PM, Hiram Clawson <[email protected]> wrote: > Add -lssl to your MYSQLLIBS environment variable. > You mysql libraries are SSL enabled. You may need > to properly install the mysql development system. > Check the output of this command on your system: > $ rpm -qa | grep -i mysql > > It should say something about MySQL-devel > > See also, helpful work around discussion for build > problems in the source tree file: > kent/src/README.building.source > > > --Hiram > > Abhishek Goel wrote: > >> Hello Hiram, >> >> At first my particular distribution was missing the libmysqlclient.a file. >> I >> managed to get that from another one of our servers and set the >> environment >> variable to its location. >> >> I used CVS to get the source tree. >> >> When I type make in the kent/src/hg/makeDb/hgTrackDb directory I get the >> following error: >> >> 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 >> hgTrackDb.o -c hgTrackDb.c >> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized >> -o /root/bin/x86_64/hgTrackDb hgTrackDb.o ../../../lib/x86_64/jkhgap.a >> ../../../lib/x86_64/jkweb.a -lm /usr/lib64/mysql/libmysqlclient.a -lz >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_close_free_options': >> (.text+0xdb5): undefined reference to `SSL_CTX_free' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_get_ssl_cipher': >> (.text+0x1155): undefined reference to `SSL_get_current_cipher' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_real_connect': >> (.text+0x3879): undefined reference to `SSL_get_peer_certificate' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_real_connect': >> (.text+0x3891): undefined reference to `X509_get_subject_name' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_real_connect': >> (.text+0x38a1): undefined reference to `X509_NAME_oneline' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_real_connect': >> (.text+0x38a9): undefined reference to `X509_free' >> /usr/lib64/mysql/libmysqlclient.a(client.o): In function >> `mysql_get_ssl_cipher': >> (.text+0x1161): undefined reference to `SSL_CIPHER_get_name' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x54): undefined reference to `SSL_new' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x68): undefined reference to `SSL_clear' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x70): undefined reference to `SSL_get_session' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x7b): undefined reference to `SSL_SESSION_set_timeout' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x86): undefined reference to `SSL_set_fd' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x99): undefined reference to `SSL_get_fd' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x105): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x112): undefined reference to `SSL_free' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `ssl_do': >> (.text+0x155): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `sslconnect': >> (.text+0x161): undefined reference to `SSL_connect' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `sslaccept': >> (.text+0x171): undefined reference to `SSL_accept' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_close': >> (.text+0x1a6): undefined reference to `SSL_set_quiet_shutdown' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_close': >> (.text+0x1ae): undefined reference to `SSL_shutdown' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_delete': >> (.text+0x1ec): undefined reference to `SSL_free' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_write': >> (.text+0x228): undefined reference to `SSL_write' >> /usr/lib64/mysql/libmysqlclient.a(viossl.o): In function `vio_ssl_read': >> (.text+0x238): undefined reference to `SSL_read' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x71): undefined reference to `SSL_CTX_new' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x8e): undefined reference to `SSL_CTX_set_cipher_list' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0xa7): undefined reference to `SSL_CTX_load_verify_locations' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0xc8): undefined reference to `SSL_CTX_use_certificate_file' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0xe7): undefined reference to `SSL_CTX_use_PrivateKey_file' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0xf7): undefined reference to `SSL_CTX_check_private_key' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x107): undefined reference to `DH_new' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x127): undefined reference to `BN_bin2bn' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x13c): undefined reference to `BN_bin2bn' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x167): undefined reference to `SSL_CTX_ctrl' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x16f): undefined reference to `DH_free' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x1a5): undefined reference to `SSL_CTX_set_default_verify_paths' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x1d5): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x1e5): undefined reference to `SSL_CTX_free' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x208): undefined reference to `SSL_load_error_strings' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x220): undefined reference to `SSL_library_init' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x225): undefined reference to `OPENSSL_add_all_algorithms_noconf' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x278): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x2d6): undefined reference to `DH_free' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x30d): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x31b): undefined reference to `SSL_CTX_free' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLFd': >> (.text+0x35d): undefined reference to `ERR_get_error_line_data' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLAcceptorFd': >> (.text+0x39d): undefined reference to `TLSv1_server_method' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLAcceptorFd': >> (.text+0x3d0): undefined reference to `SSL_CTX_ctrl' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLAcceptorFd': >> (.text+0x3e2): undefined reference to `SSL_CTX_set_verify' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLAcceptorFd': >> (.text+0x3f2): undefined reference to `SSL_CTX_set_session_id_context' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x452): undefined reference to `X509_STORE_CTX_get_current_cert' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x45a): undefined reference to `X509_get_subject_name' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x46a): undefined reference to `X509_NAME_oneline' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x4b8): undefined reference to `X509_get_issuer_name' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x4c8): undefined reference to `X509_NAME_oneline' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x4d4): undefined reference to `X509_STORE_CTX_get_error' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `vio_verify_callback': >> (.text+0x4dc): undefined reference to `X509_STORE_CTX_get_error_depth' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLConnectorFd': >> (.text+0x52d): undefined reference to `TLSv1_client_method' >> /usr/lib64/mysql/libmysqlclient.a(viosslfactories.o): In function >> `new_VioSSLConnectorFd': >> (.text+0x56f): undefined reference to `SSL_CTX_set_verify' >> collect2: ld returned 1 exit status >> make: *** [hgTrackDb] Error 1 >> >> >> >> >> Abhishek Goel >> Staff Research Associate >> Geschwind Laboratory, UCLA Neurology >> Gonda Neuroscience and Genetics Research Center #2309 >> University of California Los Angeles >> 695 Charles E. Young Dr. South >> Los Angeles, CA 90095 >> Tel: (310) 794-7537 >> Fax: (310) 267-2401 >> >> >> >> >> >> On Tue, Nov 10, 2009 at 9:11 PM, Hiram Clawson <[email protected]> >> wrote: >> >> Please give me a hint on your compile problems. >>> It should be pretty easy to build the binaries there. >>> If you are going to be running your own copy of >>> the genome browser you will want to be able to >>> build the source tree. Give me an example of >>> a failed gcc command. >>> >>> --Hiram >>> >>> Abhishek Goel wrote: >>> >>> Hello Hiram, >>>> >>>> Thank you for that information. I've been trying to compile the >>>> hgTrackDb >>>> and hgFindSpec binaries but I keep running into an error. I am trying to >>>> find some solution for the issue but I was wondering if there were any >>>> precompiled versions that you had that we could download. Is that a >>>> possibility? >>>> >>>> Thanks >>>> >>>> Abhishek >>>> >>>> >>>> Abhishek Goel >>>> Staff Research Associate >>>> Geschwind Laboratory, UCLA Neurology >>>> Gonda Neuroscience and Genetics Research Center #2309 >>>> University of California Los Angeles >>>> 695 Charles E. Young Dr. South >>>> Los Angeles, CA 90095 >>>> Tel: (310) 794-7537 >>>> Fax: (310) 267-2401 >>>> >>>> >>>> >>>> >>>> >>>> On Tue, Oct 27, 2009 at 8:35 AM, Hiram Clawson <[email protected]> >>>> wrote: >>>> >>>> Good Morning Abhishek: >>>> >>>>> You should take these tracks and make them permanent tracks >>>>> in your browser if you would like them to be available to >>>>> everyone. See these starting notes about how to load tracks >>>>> into the browser: >>>>> >>>>> http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/README.trackDb<http://genome-test.cse.ucsc.edu/%7Ekent/src/unzipped/product/README.trackDb> >>>>> < >>>>> http://genome-test.cse.ucsc.edu/%7Ekent/src/unzipped/product/README.trackDb >>>>> > >>>>> < >>>>> >>>>> http://genome-test.cse.ucsc.edu/%7Ekent/src/unzipped/product/README.trackDb >>>>> >>>>> Follow the additional references to other README files from there. >>>>> >>>>> --Hiram >>>>> >>>>> >>>>> Abhishek Goel wrote: >>>>> >>>>> Hello Jennifer, >>>>> >>>>>> Thank you for that info. Do you have any suggestions on where to >>>>>> start. >>>>>> I >>>>>> was going to see if there was any table with the list of hgsids but it >>>>>> turns >>>>>> out those are just temp ids and not really useful. >>>>>> >>>>>> Each time a BED file is loaded into the browser to create a custom >>>>>> track >>>>>> a >>>>>> new table is added to the customTrash database. The table itself is >>>>>> just >>>>>> the >>>>>> mysql version of the BED file. >>>>>> >>>>>> Thanks. >>>>>> >>>>>> Abhishek >>>>>> >>>>>> >>>>>> Abhishek Goel >>>>>> Staff Research Associate >>>>>> Geschwind Laboratory, UCLA Neurology >>>>>> Gonda Neuroscience and Genetics Research Center #2309 >>>>>> University of California Los Angeles >>>>>> 695 Charles E. Young Dr. South >>>>>> Los Angeles, CA 90095 >>>>>> Tel: (310) 794-7537 >>>>>> Fax: (310) 267-2401 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Oct 22, 2009 at 5:42 PM, Jennifer Jackson <[email protected]> >>>>>> wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> No, there is no automatically generated page. The idea of making one >>>>>>> from >>>>>>> the custom track table is a good one. >>>>>>> >>>>>>> The only alternative would be to get wiki and Sessions set up, but >>>>>>> that >>>>>>> is >>>>>>> a major project, and not worth it for just a web page view. >>>>>>> >>>>>>> Hope this helps, >>>>>>> Jennifer >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------ >>>>>>> Jennifer Jackson >>>>>>> UCSC Genome Bioinformatics Group >>>>>>> >>>>>>> ----- "Abhishek Goel" <[email protected]> wrote: >>>>>>> >>>>>>> From: "Abhishek Goel" <[email protected]> >>>>>>> >>>>>>> To: [email protected] >>>>>>>> Sent: Thursday, October 22, 2009 12:29:28 PM GMT -08:00 US/Canada >>>>>>>> Pacific >>>>>>>> Subject: [Genome] Saved custom tracks >>>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> I've just set up a Genome Browser mirror for our lab and our >>>>>>>> collaborators. >>>>>>>> I enabled the customTrash database and set up the hg.conf file so >>>>>>>> that >>>>>>>> the >>>>>>>> added customTracks are saved. However, is there a page that lists >>>>>>>> all >>>>>>>> the >>>>>>>> custom tracks that have been saved? >>>>>>>> >>>>>>>> I could just create a page that would list all the saved custom >>>>>>>> tracks >>>>>>>> from >>>>>>>> the mysql database but I thought if there is already a page I could >>>>>>>> just use >>>>>>>> that. >>>>>>>> >>>>>>>> Thanks. >>>>>>>> >>>>>>>> Abhishek >>>>>>>> >>>>>>>> Abhishek Goel >>>>>>>> Staff Research Associate >>>>>>>> Geschwind Laboratory, UCLA Neurology >>>>>>>> Gonda Neuroscience and Genetics Research Center #2309 >>>>>>>> University of California Los Angeles >>>>>>>> 695 Charles E. Young Dr. South >>>>>>>> Los Angeles, CA 90095 >>>>>>>> Tel: (310) 794-7537 >>>>>>>> Fax: (310) 267-2401 >>>>>>>> _______________________________________________ >>>>>>>> Genome maillist - [email protected] >>>>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> >>>>>>> Genome maillist - [email protected] >>>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>>>> >>>>>> >>>>>> >>>>>> >> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
