hi, as i am behind a http proxy and the biomart package tries to establish a direct mysql connectioj to the ensembl database i had no chance to test or use the biomaRt package. well, now i finally managed to install a local version of biomart (after some problems i had with different versions of mysql (i strongly recommend to use MySQL > 4.1 !)). my question is now, how and where do i have to change biomaRt source to connect to my local biomart database? another question: which mart database uses biomaRt, i assume the ensemble_mart and not the uniprot and msd mart... cheers, jo

Hi Jo, In the function martConnect you should write something like this (using the correct host,....) mart <- new("Mart", ensembl = dbConnect(drv = driver,user = user, host = host , dbname = databases$ensembl, password = password), vega = dbConnect(drv = driver,user = user, host= host, dbname = databases$vega, password = password), sequence = dbConnect(drv = driver,user = user, host = host, dbname = databases$sequence, password = password), snp = dbConnect(drv = driver,user = user, host = host, dbname = databases$snp, password = password), arrayToSpecies = arrayToSpecies, arrayToEnsembl = arrayToEnsembl ); You'll also need to change the host etc in the function listMarts listMarts <- function(host = "ensembldb.ensembl.org", user = "anonymous", password = ""){ driv <- dbDriver("MySQL", force.reload = FALSE); connection <- dbConnect(driv, user = user, host = host, password = password); If you can wait a few more hours I could send you the latest release of biomaRt in which you don't have to make changes in the source code anymore but can change host from within your R session. BioMart currently uses Ensembl_mart, snp_mart, vega_mart, and sequence_mart. It will try to connect to these marts all at once. We plan to include a way of selection so if you only use ensembl you don't have to install all other marts although these currently come together if you do a local ensembl install. best, Steffen Dipl.-Ing. Johannes Rainer wrote: > hi, > > as i am behind a http proxy and the biomart package tries to establish > a direct mysql connectioj to the ensembl database i had no chance to > test or use the biomaRt package. > well, now i finally managed to install a local version of biomart > (after some problems i had with different versions of mysql (i > strongly recommend to use MySQL > 4.1 !)). my question is now, how and > where do i have to change biomaRt source to connect to my local > biomart database? > another question: which mart database uses biomaRt, i assume the > ensemble_mart and not the uniprot and msd mart... > > cheers, jo > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Hi Steffen, thanks for your great support! i will wait for the new package... thanks, jo Quoting Steffen Durinck <sdurinck@ebi.ac.uk>: > Hi Jo, > > In the function martConnect you should write something like this > (using the correct host,....) > > mart <- new("Mart", > ensembl = dbConnect(drv = driver,user = user, host = > host , dbname = databases$ensembl, password = password), > vega = dbConnect(drv = driver,user = user, host= host, > dbname = databases$vega, password = password), > sequence = dbConnect(drv = driver,user = user, host = > host, dbname = databases$sequence, password = password), > snp = dbConnect(drv = driver,user = user, host = host, > dbname = databases$snp, password = password), > arrayToSpecies = arrayToSpecies, > arrayToEnsembl = arrayToEnsembl > ); > > You'll also need to change the host etc in the function listMarts > > listMarts <- function(host = "ensembldb.ensembl.org", user = > "anonymous", password = ""){ > > driv <- dbDriver("MySQL", force.reload = FALSE); > connection <- dbConnect(driv, user = user, host = host, password = > password); > > > If you can wait a few more hours I could send you the latest release > of biomaRt in which you don't have to make changes in the source code > anymore but can change host from within your R session. BioMart > currently uses Ensembl_mart, snp_mart, vega_mart, and sequence_mart. > It will try to connect to these marts all at once. We plan to > include a way of selection so if you only use ensembl you don't have > to install all other marts although these currently come together if > you do a local ensembl install. > > best, > Steffen > > > > Dipl.-Ing. Johannes Rainer wrote: > >> hi, >> >> as i am behind a http proxy and the biomart package tries to >> establish a direct mysql connectioj to the ensembl database i had no >> chance to test or use the biomaRt package. >> well, now i finally managed to install a local version of biomart >> (after some problems i had with different versions of mysql (i >> strongly recommend to use MySQL > 4.1 !)). my question is now, how >> and where do i have to change biomaRt source to connect to my local >> biomart database? >> another question: which mart database uses biomaRt, i assume the >> ensemble_mart and not the uniprot and msd mart... >> >> cheers, jo >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >

hi steffen, i installed the new package, but i have a slightly problem... i can't connect to the mart database... i write you the error message that i got: Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not connect anonymous@ensembldb.ensembl.org on dbname "(null)" i tried to connect to the database using the dbConnect method and it worked, so i think it may be a problem with the dbname = databases$ensembl... i have installed the ensembl_mart_30, so the database has the same name. i hope the database i installed is the right one... i downloaded the whole directory ensembl_mart_30 from ensembl: ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ and installed this according to the howto from http://www.ebi.ac.uk/biomart/DB_install.html i checked again the martConnect function and am afraid that i do not have the right database... if there should be tables in there called affy_hg_u133_plus_2 i get a problem, because i do not have those... can you please help me to find the right database to download? what name should this database have? thanks, jo Quoting sdurinck@ebi.ac.uk: > Hi Jo, > > No problem;) > > In attach the biomaRt version with changing host possibilities. > Would you mind to test if it really works? I haven't got a local Ensembl > install so can't really test it but it should work. > > you should now connect using the function: > > mart<-martConnect(host = "your host",user = "username", > password="yourpasswd") > > Can you let me know if it works or if you run into troubles? > > Cheers, > Steffen > > > >> Hi Steffen, > >> thanks for your great support! i will wait for the new package... > >> thanks, jo > >

thanks Steffen, i installed it and i can connect to the database :) ... but i get the following lovely exception when i test the db: mart <- martConnect(host="10.3.80.23",user="jo",password="123") - Connected to: ensembl_mart_30 - > getGene(id="201131_s_at",array="hgu133plus2",mart=mart) Error in mysqlExecStatement(conn, statement, ...) : RS-DBI driver: (could not run statement: Table 'ensembl_mart_30.NA_gene_ensembl__xref_affy_hgu133plus2__dm' doesn't exist) it seems that i have a littl eproblem with the species, somehow the "hsapiens" is missing in the table name... any idea why? cheers, jo Quoting Steffen Durinck <sdurinck@ebi.ac.uk>: > Jo, > > In attach the fixed biomaRt version. Using my local Ensembl database > now works without internet connection;) > I hope we can get your installation working this time! Best, > Steffen > > > Dipl.-Ing. Johannes Rainer wrote: > >> Hi Steffen, >> >> i checked the database, the database should be ok (i have installed >> the whole ensembl_mart_30, but without the vega_mart and the >> snp_mart, because i didn't find them...). my ensembl_mart_30 has the >> hsapiens... affy... table. but when i try to connect to the database >> (which is not really installed locally at my notebook, but on our >> server) i get alwys the same exception >> >> Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >> connect anonymous@ensembldb.ensembl.org on dbname "(null)" >> ) >> >> have you tried to connect to your local database with the network >> cable unplugged, so that you also have no connection to the ensembl >> db? >> the biomaRt package i have installed has the version 1.02, is this >> the right one? >> >> thanks for your help! >> cheers, jo >> >> >> Quoting sdurinck@ebi.ac.uk: >> >>> Hi Jo, >>> >>> I got things working here... >>> As I don't have enough space on my laptop I did a minimal install using >>> only two tables as a test. >>> >>> in mysql: >>> >>> create database ensembl_mart_30 >>> >>> then in your command line: >>> >>> mysql -D ensembl_mart_30 -u DBMAN -p < ensembl_mart_30.sql >>> >>> mysqlimport -L -u DBMAN -p ensembl_mart_30 >>> hsapiens_gene_ensembl__gene__main.txt.table >>> >>> mysqlimport -L -u DBMAN -pDBMAN ensembl_mart_30 >>> sapiens_gene_ensembl__xref_affy_hg_u133_plus_2__dm.txt.table >>> >>> mysqlimport -L -u DBMAN -pDBMAN ensembl_mart_30 >>> meta_release_info.txt.table >>> >>> now I have a mini ensembl install with the human gene info and mapping of >>> the affy hgu133plus2 id's to ensembl. To work you also need the >>> meta_release_info table. >>> >>> in R I could do now: >>> >>> mart<-martConnect(host="localhost",user="DBMAN", password="DBMAN") >>> getGene(id="201131_s_at",array="hgu133plus2",mart=mart) >>> >>> and the getGene function retrieved the correct result. >>> >>> Did you installed ensembl the same way? it's important that your database >>> has the name ensembl_mart_30 (or with any other version number) otherwise >>> it won't work. >>> >>> Cheers, >>> Steffen >>> >>> hi steffen, >>> >>> i installed the new package, but i have a slightly problem... i can't >>> connect to the mart database... i write you the error message that i got: >>> >>> Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not connect >>> anonymous@ensembldb.ensembl.org on dbname "(null)" >>> >>> i tried to connect to the database using the dbConnect method and it >>> worked, so i think it may be a problem with the dbname = >>> databases$ensembl... i have installed the ensembl_mart_30, so the database >>> has the same name. i hope the database i installed is the right one... i >>> downloaded the whole directory ensembl_mart_30 from ensembl: >>> >>> ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ >>> >>> and installed this according to the howto from >>> >>> http://www.ebi.ac.uk/biomart/DB_install.html >>> >>> i checked again the martConnect function and am afraid that i do not have >>> the right database... if there should be tables in there called >>> affy_hg_u133_plus_2 i get a problem, because i do not have those... >>> >>> can you please help me to find the right database to download? what name >>> should this database have? >>> >>> thanks, jo >>> >> >> >> >> > >

thanks, it works! i had to change the hgu133plus2 into hg_u133_plus_2 and it worked then. thanks for all your help :) cheers, jo Quoting Steffen Durinck <sdurinck@ebi.ac.uk>: > I forgot to mention that in this version we started using the ensembl > names for species so now to use homo sapiens you should use hsapiens > instead of homo_sapiens. A list of valid species names can be > obtained using the function getSpecies. Also we use the ensembl > names of the affy arrays. > hgu95av2 now becomes hg_u95av2. Again a list of valid names can be > obtained using the function getAffyArrays. > > best, > Steffen > > Dipl.-Ing. Johannes Rainer wrote: > >> Hi Steffen, >> >> i checked the database, the database should be ok (i have installed >> the whole ensembl_mart_30, but without the vega_mart and the >> snp_mart, because i didn't find them...). my ensembl_mart_30 has the >> hsapiens... affy... table. but when i try to connect to the database >> (which is not really installed locally at my notebook, but on our >> server) i get alwys the same exception >> >> Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not >> connect anonymous@ensembldb.ensembl.org on dbname "(null)" >> ) >> >> have you tried to connect to your local database with the network >> cable unplugged, so that you also have no connection to the ensembl >> db? >> the biomaRt package i have installed has the version 1.02, is this >> the right one? >> >> thanks for your help! >> cheers, jo >> >> >> Quoting sdurinck@ebi.ac.uk: >> >>> Hi Jo, >>> >>> I got things working here... >>> As I don't have enough space on my laptop I did a minimal install using >>> only two tables as a test. >>> >>> in mysql: >>> >>> create database ensembl_mart_30 >>> >>> then in your command line: >>> >>> mysql -D ensembl_mart_30 -u DBMAN -p < ensembl_mart_30.sql >>> >>> mysqlimport -L -u DBMAN -p ensembl_mart_30 >>> hsapiens_gene_ensembl__gene__main.txt.table >>> >>> mysqlimport -L -u DBMAN -pDBMAN ensembl_mart_30 >>> sapiens_gene_ensembl__xref_affy_hg_u133_plus_2__dm.txt.table >>> >>> mysqlimport -L -u DBMAN -pDBMAN ensembl_mart_30 >>> meta_release_info.txt.table >>> >>> now I have a mini ensembl install with the human gene info and mapping of >>> the affy hgu133plus2 id's to ensembl. To work you also need the >>> meta_release_info table. >>> >>> in R I could do now: >>> >>> mart<-martConnect(host="localhost",user="DBMAN", password="DBMAN") >>> getGene(id="201131_s_at",array="hgu133plus2",mart=mart) >>> >>> and the getGene function retrieved the correct result. >>> >>> Did you installed ensembl the same way? it's important that your database >>> has the name ensembl_mart_30 (or with any other version number) otherwise >>> it won't work. >>> >>> Cheers, >>> Steffen >>> >>> hi steffen, >>> >>> i installed the new package, but i have a slightly problem... i can't >>> connect to the mart database... i write you the error message that i got: >>> >>> Error in mysqlNewConnection(drv, ...) : RS-DBI driver: (could not connect >>> anonymous@ensembldb.ensembl.org on dbname "(null)" >>> >>> i tried to connect to the database using the dbConnect method and it >>> worked, so i think it may be a problem with the dbname = >>> databases$ensembl... i have installed the ensembl_mart_30, so the database >>> has the same name. i hope the database i installed is the right one... i >>> downloaded the whole directory ensembl_mart_30 from ensembl: >>> >>> ftp://ftp.ensembl.org/pub/current_mart/data/mysql/ >>> >>> and installed this according to the howto from >>> >>> http://www.ebi.ac.uk/biomart/DB_install.html >>> >>> i checked again the martConnect function and am afraid that i do not have >>> the right database... if there should be tables in there called >>> affy_hg_u133_plus_2 i get a problem, because i do not have those... >>> >>> can you please help me to find the right database to download? what name >>> should this database have? >>> >>> thanks, jo >>> >> >> >> >> > >