[galaxy-user] upload large data set
Dear Sir/Madam, I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq file into galaxy, but failed. Below is the error message. OverflowError: signed integer is greater than maximum How could I upload large data files into galaxy and process the data? Any information from you would be quite appreciated. Thanks, Dicty ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Join and Sort in Galaxy
Hi Felix, You are correct, the Sort Join functions are unix based. Even so, sorting before joining is not required and will not make the Join tool run faster. Actual performance will depend on the size the data and the current server load. If a tool job (any) is taking what seems to be a very long time, please try a re-run. If it is still a problem, feel free to send a shared linked to your history and we can take a look to make certain nothing server-side is going on. A method to allow direct user tracking of progress is something the team has been discussing for some time. It is great idea and is on our priority list. Thanks for using Galaxy! Best, Jen Galaxy team On 2/24/11 1:32 AM, Felix Hammer wrote: Hello, I have some questions about the Join and Sort tools in Galaxy. How are they implemented? Just the standard unix sort and join? I have a quite large tab file (~1,5 million lines), I want to join with a somewhat smaller file (~20 000 lines). How long will this approximately take? Is there a way to view the progress? Can I gain performance if do a sort on the column I want to join? thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] upload large data set
Hello Dicty, Is this using the FTP upload method? If not, please try that as an alternative to browser upload (required for large files). Instructions are on the Get Data - Upload tool. For a desktop FTP client, we recommend using Mozilla http://www.mozilla.org/. Hopefully this helps, Best, Jen Galaxy team On 3/4/11 8:27 AM, Yanji Xu wrote: Dear Sir/Madam, I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq file into galaxy, but failed. Below is the error message. OverflowError: signed integer is greater than maximum How could I upload large data files into galaxy and process the data? Any information from you would be quite appreciated. Thanks, Dicty ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Map with Bowtie job is waiting to run for more than 1 hour...
Hello Daniel, There are no known problems with the tool or the cluster. Sounds like your job was queued up last night. Has it it started/completed by now? Please try a re-run first to see if it will move into running and if it continues to stall in waiting after some time (hour or so), please email back with a shared link to your history and so can take a look at the specific run and diagnose further here. We look forward to your feedback, even if it is just that things are running OK now! Best, Jen Galaxy team On 3/1/11 8:07 PM, Daniel Fernandez wrote: Hi, I tried running map with bowtie but it says: job is waiting to run... any suggestions? Thanks! ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
