- galaxy-user - lists.galaxyproject.org

Mysql backend setup
by Stein, Olaf 09 Mar '10

09 Mar '10

Hi all, Very new to galaxy and trying to setup an instance here with mysql as the backend database. I added this line: mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock To the universe_wsgi.ini file Where do I define the dbuser, password and database that I want to use? And what else do I need to do, for instance create the schema, etc? Thanks Olaf ------------------------- Olaf Stein DBA Battelle Center for Mathematical Medicine Nationwide Children's Hospital, The Research Institute 700 Children's Drive 43205 Columbus, OH phone: 1-614-355-5685 cell: 1-614-843-0432 email: olaf.stein(a)nationwidechildrens.org "I consider that the golden rule requires that if I like a program I must share it with other people who like it." Richard M. Stallman

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problem with getting the tables up in Profile Annotations
by CHAN Chee Seng 08 Mar '10

08 Mar '10

Hi, I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the "Tables to Use" to be displayed on the web interface. I have looked at the following files. 1. annotation_profiler_options.xml 2. annotation_profiler_valid_builds.txt I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line, hg18 which is fine since I am starting with human. Where do I specify the location of my hg18? Please let me know if you need more information. Thanks for your help. Best regards, Chee Seng, Chan Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065 ------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------

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Fwd: [galaxy-dev] Fwd: Protein names
by Anton Nekrutenko 06 Mar '10

06 Mar '10

Begin forwarded message: > From: Yu Lin <linikujp(a)gmail.com> > Date: March 5, 2010 7:21:09 PM EST > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: Re: [galaxy-dev] Fwd: [galaxy-user] Protein names > > Hi, > > "My assumption was that people would load their favorite gene > annotations " > from the ontology's point of view: "favorite gene annotations" will be > dangerous. > "use an "interval" join to attach the desired names".... what dose > it mean? > > Dangerous means that later there will be a lot misunderstandings, > which is not convenient for biologist. > I think it's better to use a standard. > OR > favorite gene annotations > always bound to > a standard gene annotations. > > Thanks, > Lin. > > ************************************************* > Yu Lin > Ph.D.,M.D. > > Genome Resource and Analysis Unit, > Genomics Laboratory, > Center for Developmental Biology, > RIKEN > > TEL&FAX 0081-78-3063048 > Extension:4232 > Email: linyu(a)cdb.riken.jp > ************************************************* > > > > 2010/3/6 Anton Nekrutenko <anton(a)bx.psu.edu>: >> >> >> Begin forwarded message: >> >> From: webb(a)bx.psu.edu >> Date: March 5, 2010 1:44:01 PM EST >> To: Tjaart de Beer <tdebeer(a)gmail.com> >> Cc: Anton Nekrutenko <anton(a)bx.psu.edu>, Webb Miller >> <webb(a)bx.psu.edu>, >> Aakrosh Ratan <ratan(a)cse.psu.edu> >> Subject: Re: Fwd: [galaxy-user] Protein names >> Hi, >> >> The gene annotations are from RefSeq. As we processed the SNPs with >> tools >> such as PolyPhen and Sift, we sometimes had to use other names. My >> assumption was that people would load their favorite gene >> annotations into >> Galaxy and use an "interval" join to attach the desired names. Can >> you do >> something like that? Or is the problem that you need to deal with >> alternate >> splice forms? >> >> Please keep asking until you have everything working. If necessary, >> I can >> regenerate the file with other protein names. Thanks for your >> patience. >> >> --Webb >> >> >> Quoting Anton Nekrutenko <anton(a)bx.psu.edu>: >> >> Webb: >> >> The question here is on where the protein names come from. Can you >> elaborate, so I send him a reply. >> >> Thanks, >> >> anton >> >> >> >> Begin forwarded message: >> >> From: Tjaart de Beer <tdebeer(a)gmail.com> >> >> Date: March 5, 2010 7:34:13 AM EST >> >> To: galaxy-user(a)bx.psu.edu >> >> Subject: [galaxy-user] Protein names >> >> Hi >> >> I am trying to parse some data from the Bushmen dataset and have a >> question. >> >> Where do you get the protein names from? It does not correspond 100% >> >> to the UniProt ID field in Uniprot entries nor is it Uniprot AC >> >> numbers. Is there some kind of mapping I can use to get the >> >> appropriate names or Uniprot entries? Would you be able to provide >> >> with this mapping? I have been going through the Uniprot website >> >> rather extensively and have failed to find any such downloadable >> >> mapping. Hope you can help! >> >> Thanks! >> >> Dr. Tjaart de Beer >> >> Thornton group >> >> EMBL-EBI >> >> Cambridge >> >> _______________________________________________ >> >> galaxy-user mailing list >> >> galaxy-user(a)lists.bx.psu.edu >> >> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> Anton Nekrutenko >> >> http://nekrut.bx.psu.edu >> >> http://usegalaxy.org >> >> >> >> >> >> >> >> >> Anton Nekrutenko >> http://nekrut.bx.psu.edu >> http://usegalaxy.org >> >> >> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> > > > > -- > Yu LIN. > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Fwd: Protein names
by Anton Nekrutenko 05 Mar '10

05 Mar '10

Begin forwarded message: > From: webb(a)bx.psu.edu > Date: March 5, 2010 1:44:01 PM EST > To: Tjaart de Beer <tdebeer(a)gmail.com> > Cc: Anton Nekrutenko <anton(a)bx.psu.edu>, Webb Miller > <webb(a)bx.psu.edu>, Aakrosh Ratan <ratan(a)cse.psu.edu> > Subject: Re: Fwd: [galaxy-user] Protein names > > Hi, > > The gene annotations are from RefSeq. As we processed the SNPs with > tools such as PolyPhen and Sift, we sometimes had to use other > names. My assumption was that people would load their favorite gene > annotations into Galaxy and use an "interval" join to attach the > desired names. Can you do something like that? Or is the problem > that you need to deal with alternate splice forms? > > Please keep asking until you have everything working. If necessary, > I can regenerate the file with other protein names. Thanks for your > patience. > > --Webb > > > Quoting Anton Nekrutenko <anton(a)bx.psu.edu>: > >> Webb: >> >> The question here is on where the protein names come from. Can you >> elaborate, so I send him a reply. >> >> Thanks, >> >> anton >> >> >> >> Begin forwarded message: >> >>> From: Tjaart de Beer <tdebeer(a)gmail.com> >>> Date: March 5, 2010 7:34:13 AM EST >>> To: galaxy-user(a)bx.psu.edu >>> Subject: [galaxy-user] Protein names >>> >>> Hi >>> >>> I am trying to parse some data from the Bushmen dataset and have >>> a question. >>> >>> Where do you get the protein names from? It does not correspond 100% >>> to the UniProt ID field in Uniprot entries nor is it Uniprot AC >>> numbers. Is there some kind of mapping I can use to get the >>> appropriate names or Uniprot entries? Would you be able to provide >>> with this mapping? I have been going through the Uniprot website >>> rather extensively and have failed to find any such downloadable >>> mapping. Hope you can help! >>> >>> Thanks! >>> >>> Dr. Tjaart de Beer >>> Thornton group >>> EMBL-EBI >>> Cambridge >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> Anton Nekrutenko >> http://nekrut.bx.psu.edu >> http://usegalaxy.org >> >> >> >> > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Protein names
by Tjaart de Beer 05 Mar '10

05 Mar '10

Hi I am trying to parse some data from the Bushmen dataset and have a question. Where do you get the protein names from? It does not correspond 100% to the UniProt ID field in Uniprot entries nor is it Uniprot AC numbers. Is there some kind of mapping I can use to get the appropriate names or Uniprot entries? Would you be able to provide with this mapping? I have been going through the Uniprot website rather extensively and have failed to find any such downloadable mapping. Hope you can help! Thanks! Dr. Tjaart de Beer Thornton group EMBL-EBI Cambridge

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pre-loading data on server
by Brent Pedersen 26 Feb '10

26 Feb '10

hi, i have an instance of galaxy running on my own server. i'd like to have it preloaded with data and have that available to the users. say: thaliana_v9.gff and thaliana_v9.fasta . how do i do that? i've edited tool-data/faseq.loc and added: thaliana_v9 /opt/src/galaxy-server/localdata/fastas/ what else (or other) should i do? thanks, -brent

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Text editor
by Jelle Scholtalbers 25 Feb '10

25 Feb '10

Hi, is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful. Cheers, Jelle

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zip vs. gzip
by Pieter Neerincx 10 Feb '10

10 Feb '10

Hi, Can someone help me understand the automagic (un)zipping in Galaxy? In my universe_wsgi.ini there an option to enable gzip compression like this: # ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer ) # but you may also turn on Paste's built-in gzip compressor by uncommenting the following lines # and also the 'filter-with = gzip' line under [app:main]. This will reduce network traffic # and should speed up the interface, especially the visualization module. # [filter:gzip] use = egg:Paste#gzip ... filter-with = gzip 1. I cannot find instructions on how to enable gzip compression in Apache at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, but I have enabled "Paste's built-in gzip compressor" and that does not generate errors, so I guess it works. 2. This is not the part that is responsible for automatically detecting *.gz files and unzipping them, or is it? Enabling or disabling the code above does not affect automagic unzipping of uploaded *.gz, which works for me with or without the code above. 2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip.... Cheers, Pi

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Novice questions
by Mariette 08 Feb '10

08 Feb '10

Hi, I'm currently using ergatis as workflow manager, and I'm looking at the differences between ergatis and galaxy. In order maybe to migrate to galaxy. One really important feature to me is the ability of ergatis to iterate against file liste. I haven't seen anything like this in galaxy, am I mistaking ? Other point there is a way to make galaxy using local files instead of importing all files on the server ? And finaly I was wondering if there is a way to configure galaxy, so the outputs are stored to the ldap-user home directory ? thanks for your reply, Jerome

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Re: [galaxy-user] taxBuilder executable
by Anton Nekrutenko 08 Feb '10

08 Feb '10

Edward: The binaries are here: http://dist.g2.bx.psu.edu/ Let us know if you have trouble. Thanks, anton galaxy team On Feb 5, 2010, at 10:31 PM, Edward Kirton wrote: > oops, i should have specified that this is on my local install > > > On Feb 5, 2010, at 6:03 PM, anton(a)bx.psu.edu wrote: > >> Ed: >> >> Do you see this on your local install or on the main site? >> >> anton >> galaxy team >> >> >> >>> taxonomy/gi2taxonomy.py gives me this error: >>> >>> /bin/sh: taxBuilder: command not found >>> >>> what is this taxBuilder program and where do i find it? i didn't >>> find >>> anything via google >>> >>> thanks! >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> >> > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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