[galaxy-user] Fwd: Question about FTP
- Forwarded message from Noushin Ghaffari noushin.ghaff...@gmail.com - Date: Mon, 7 Mar 2011 09:09:13 -0600 From: Noushin Ghaffari noushin.ghaff...@gmail.com To: dbad...@bio.cse.psu.edu Subject: Question about FTP Dear Galaxy team, Firstly, thank you very much for the great tools. I am working on a large dataset and need to upload it to Galaxy via FTP. I used ftp://main.g2.bx.psu.edu but I cannot login. I used my email, my public name on Galaxy and just simple my name, but none of them worked. Can you please help me to know how can I login to upload my file? Here is my inofrmation: email: noushin.ghaff...@gmail.com public name: me-on-galaxy I appreciate you help and time in advance. Noushin - End forwarded message - ___ 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/
[galaxy-user] BED-to-GFF: option for gff3 format
Hi Galaxy developers, Any plans on adding a gff3 format option to BED-to-GFF? I found a BED-to-GFF3 converter at the Rätsch lab's instance of Galaxy (http://galaxy.tuebingen.mpg.de/). Any plans on making this converter more widely available? Karen :) Dept of Plant Biology University of Minnesota___ 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] GTF-to-GFF3
Hi Galaxy developers, Any plans on adding a GTF-to-GFF3 format conversion? This converter is at the Rätsch lab's instance of Galaxy (http://galaxy.tuebingen.mpg.de/). Could it be made more widely available? Karen :) Dept of Plant Biology University of Minnesota___ 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/
[galaxy-user] Bowtie Job doesn't start
Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Felix ___ 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/
[galaxy-user] irc channel for galaxy
Hey guys, Is there an irc channel for galaxy? I googled for galaxy irc but all I see in the first fifty results are entries for the samsung galaxy (which is an excellent phone ;) Best Regards, George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a ___ 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] Fwd: Need a generous help regarding uploading
Hi Vasu, Very sorry to hear that you are still having problems. Have you been able to do the update? It was not clear from your email. The latest is: http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ca0c4ad2bb39 When you reply, could you note which revision you are using (perhaps you are pulling from galaxy-central instead?) Thanks for helping us to diagnose the problem, Jen Galaxy team On 1/3/11 12:05 PM, vasu punj wrote: NO I am still unable to get it through. Any help in this regard will be apprceiated. Vasu --- On *Mon, 1/3/11, Jennifer Jackson /j...@bx.psu.edu/* wrote: From: Jennifer Jackson j...@bx.psu.edu Subject: Re: [galaxy-user] Fwd: Need a generous help regarding uploading To: vasu punj pu...@yahoo.com Cc: galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edu Date: Monday, January 3, 2011, 1:59 PM Hello Vasu, Are you still having problems? Or did this other reply help? http://gmod.827538.n3.nabble.com/Bam-file-after-Tophat-run-td2089789.html#a2092204 If the problem is persistent, Galaxy needs to be updated to get better UI support for downloading BAM files. Hopefully the problem can be resolved, but please let us know if you need more help. Thanks! Jen Galaxy team On 12/15/10 12:23 PM, vasu punj wrote: I have submited your email to share job 31 and 25 are the Tophat runs which I am trying to save as bam files from Floppy icon. The job is run on our University cluster. I have alos enclosed screen shot for your ready reference. vasu --- On *Wed, 12/15/10, Jennifer Jackson /j...@bx.psu.edu Hello Asifullah, It would be helpful if you would be able to share your history. Please note which exact datasets (by number) you are having problems saving. Use Options - Share or Publish - click on the button to Share via link and then email that to me. Thank you, Jen Galaxy team On 12/15/10 7:56 AM, vasu punj wrote: I have done the same it gav eme bam index file when i removed the extension index or as such it come out to be not right bam file format as recognized by various tools Thanks Date: Wednesday, December 15, 2010, 9:52 AM Hello Asifullah, Click on the save icon for the dataset to initiate a download. This icon is shaped like a little purple disk on the very left side of the dataset's box in the right history pane. Hopefully this is helpful, Thank you, Jen Galaxy team On 12/15/10 7:47 AM, vasu punj wrote: Hi, Can we save Bam file from Tophat out put if so how can we do that please. Thanks. Date: Wednesday, December 15, 2010, 9:38 AM Hello Asifullah, The Galaxy tool Get Data - Upload File has instructions for uploading data to the FTP server. We recommend using the 3rd party utility FileZilla as a desktop FTP client. http://file-zilla.com/ Hopefully this will get you started, Best! Jen Galaxy team ps: In the future, if you could send questions directly to galaxy-u...@bx.psu.edu *Subject: **Need a generous help regarding uploading* Dear All, I am in trouble to upload 1.2Gb illumine data on Galaxy page for subsequent assembling and analysis steps. I am basically a biologist and new regarding utility of modern bioinformatics tools. some one have suggested to upload first your data on a http web page then it would be easy to be uploaded on GALaxy. But it is also not possible for me as having little computer knowledge. So could some one help me generously regarding these issue. I will highly appreciate his/her help. Regards Asifullah Khan ___ galaxy-user mailing list galaxy-user@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:
Re: [galaxy-user] Bowtie Job doesn't start
Felix Hammer wrote: Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Hi Felix, It looks like the reservation on the cluster which runs bowtie jobs isn't working at the moment and there's some contention for resources. I've reported the bug to the folks who maintain this cluster and hopefully it'll be resolved shortly. --nate Felix ___ 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/ ___ 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] Adding the Hydra genome to Galaxy
Thanks Rob, This definitely helps - we appreciate the additional info. This is on our high-priority list and Kelly will get back to you if we have more questions. Best, Jen On 3/7/11 1:23 PM, Rob Steele wrote: Hi Jen, The easiest way to refer to this genome would be Hydra_JCVI. This way we know it is the JCVI assembly (ABRM). ACZU is a separate assembly that was done at Berkeley. Including the two mitochondrial genomes would be a good idea. The many WGS submissions under ABRM are the scaffolds/contigs from the JCVI assembly. Because we were unable to obtain long-insert clones (e.g. BACs), the assembly is more fragmented than is typical for a metazoan genome assembly, and thus it has more scaffolds/contigs than is typical. Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 3/7/11 1:12 PM, Jennifer Jackson wrote: Hi Rob, The project ABRM links to several thousand individual WGS submissions. Are there scaffolds or some type of assembled sequence available? Or, perhaps there an alternate source? Also, did you want us to include the two mitochondrial genomes from NCBI in the main assembly (once we have it?). This is common for us to do, but not required. And finally, if there is a short-hand name for the genome that you and the Hydra community use, we can assign that as the short-label for the genome. Otherwise, we just use the Genus_species_source_date for the label. Some way to distinguish from ACZU seems important. Thanks Rob, we look forward to your feedback. Jen On 3/6/11 4:21 PM, Rob Steele wrote: Hi Jen, How are things progressing with the Hydra genome? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 2/15/11 6:17 AM, Jennifer Jackson wrote: Hello Rob, This genome is being worked on right now and should be available soon. Please feel free to check back a few weeks again for an update if you do not see it by then. Thanks! Jen Galaxy team On 2/14/11 3:20 PM, Rob Steele wrote: Hi Jen et al., Sorry to be a pest, but do you have an estimate for when the Hydra genome will be added to Galaxy? Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 1/3/11 12:53 PM, Jennifer Jackson wrote: Hello Rob, We will add this to our to-do list for new genomes. Thanks for sending the Genbank information! Next time, if you could send requests to galaxy-user, that would be very helpful for the team. Best, Jen Galaxy team On 1/3/11 12:37 PM, Rob Steele wrote: Hi Jennifer, Would it be possible to get the Hydra genome assembly added to Galaxy? It has been published and is available in GenBank under accession number ABRM. Cheers, Rob Rob Steele, Ph.D. Professor D240 Medical Sciences I Department of Biological Chemistry School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page -- 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/
