Please note the discussion about MySQL database permissions
in the source tree file:
src/product/README.mysql.setup
--Hiram
Jennifer Jackson wrote:
> Hello,
> It looks as if permission to create tables in the database has not been
> granted to you (or the user name you are using). Confirm with your DBA that
> your user name has create/modify/drop table permissions. Or, perhaps there is
> no disc space?
> Jennifer
>
> ------------------------------------------------
> Jennifer Jackson
> UCSC Genome Bioinformatics Group
>
> ----- "Abhishek Goel" <[email protected]> wrote:
>
>> From: "Abhishek Goel" <[email protected]>
>> To: "Hiram Clawson" <[email protected]>
>> Cc: [email protected]
>> Sent: Thursday, November 12, 2009 3:00:31 PM GMT -08:00 US/Canada Pacific
>> Subject: Re: [Genome] Saved custom tracks
>>
>> 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
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
