- galaxy-user - lists.galaxyproject.org

Problem Joining Two Datasets
by Kim Spradling 25 Jan '13

25 Jan '13

Good Afternoon, I have been having problems with my Galaxy account. The upload issue I was having has been fixed, but now I can't seem to join two datasets. I have checked both text files that I want to join to ensure they have common columns, but there are no options available when I try the drop-down menu to select a sheet to join. I also get an error message stating "Either you are not allowed to view this history or the owner of this history has not made it accessible" when I first try to view one of my other saved histories, but then the files eventually appear for that saved history. Thanks, Kim

2 1

bed file error
by ＳＣＨＥＩＮ　ＡＬＥＫＳ 24 Jan '13

24 Jan '13

Dear Galaxy users, I made a bed file from BAM for some farther analysis. Original BAM file could be nicely displayed in UCSC browser as well as in trackster. However, resulting bed file cannot be taken into UCSC-web page just stops loading without any message. Trackster returns message: "Dataset cannot be displayed due to an error" When I press "view error" button the page says "Killed". Is there any way to fix this? Best Aleks

2 1

bwa and bowtie not working
by naveed ahmed 24 Jan '13

24 Jan '13

Dear Sir/Madam Greetings, This is to inform you that i am the user of galaxy user with an user id naveedbio(a)yahoo.com where as when i run NGS Mapping, for my sample with BWA or Bowtie illumina, it keep on job waiting for more than 24-48hrs, even though the time pass the application is not working. I tried with other samples even though the problem is persisting. Concerning this i request you to let me how to solve this problem. your return confirmation would be highly appreciable... with warm regards Naveed Ahmed Syed email: naveedbio(a)yahoo.com PReduce, Reuse, Recycle, Respect - Think before you print.

2 1

Search software on public Galaxy servers
by Bernardo Bello 23 Jan '13

23 Jan '13

Hi community, Due to the increasing Galaxy public servers PublicGalaxyServers<http://wiki.galaxyproject.org/PublicGalaxyServers> it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible? Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * *

2 1

Runtime data?
by Joshua Orvis 23 Jan '13

23 Jan '13

Maybe this is in a simple place and I'm missing it, but where can I find simple runtime data for both individual tools and larger workflow executions? I have run several different versions of a saved history using the API and want to now see how the runtimes differ between them. It can be using the interface or API, that part doesn't matter. I just don't see how to look at a saved history and get any runtime statistics. Regards - Joshua

2 1

long waiting time for Bowtie jobs?
by Suzie Hight 23 Jan '13

23 Jan '13

Hello all, I have several Bowtie jobs that have been sitting in the queue for about 24 hours now - is there anything I may have done wrong to cause the long wait time? Thanks, Suzie Hight Suzie K. Hight, M.S. Graduate Research Assistant Minna Laboratory Hamon Center for Therapeutic Oncology 6000 Harry Hines Blvd Dallas, TX 75390 (214) 648-4909 ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 1

Upload files not working?
by Daniel Sher 22 Jan '13

22 Jan '13

Hello Galaxy team – the upload files tool does not seem to be working in the last few hours (small jobs in list but not running). Is there a problem with the server? Thanks Daniel -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel Office +972-4-8240731 Lab +972-4-8288961 email: dsher(a)univ.haifa.ac.il http://marsci.haifa.ac.il/mce

4 3

"spot" EC2 instances for Galaxy?
by Andrew Norman 18 Jan '13

18 Jan '13

Hi I'm wondering if anyone has had experience running Galaxy using the Amazon "spot" EC2 instances? These instances are charged based on a bid placed by the user, and only run when the bid exceeds exceeds the current spot price. In other words, you pay a significantly reduced rate for cloud capacity but it runs intermittently. This is OK for certain applications but I'm not sure how that will work for Galaxy. Specifically, I'm interested in using Galaxy for Tophat analysis of RNA seq datasets. Any insight that anyone has will be helpful. Thanks! Andy

2 1

Workflows
by Neil.Burdett＠csiro.au 18 Jan '13

18 Jan '13

Hi Sorry if these questions are obvious but I just don't know how to find the answers. I'm trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I've got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I've created workflow but don't know how to access this key. Also in the first example it states <galaxy_url>/api/workflows However I don't have the "api/workflows" directory structure in my galaxy-dist, do I need to create this? Thanks Neil

4 3

Login problems
by Jennifer Jackson 18 Jan '13

18 Jan '13

Myself and a co-worker are both having issues with uploading files on to our galaxy accounts through the FTP server. We can get our files transferred onto the FTP, but when we click "Get Data" and checkmark them to be loaded on the account, they sit indefinitely in the work queue. Both of us are having this issue on two separate accounts. Any idea what is going on with this? > > Thanks! > > Abhi

1 0