[galaxy-user] Galaxy Help
1. To Whom it May Concern: I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this. Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy. Thank you for your time, -- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914 ___ 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] Galaxy Help
Hi John, The current link is: http://wiki.galaxyproject.org/FTPUpload We changed our wiki base and many of the older links do not redirect. I'll let our wiki admin Dave know about this and see what can be done. If this comes up again soon, the base always redirects to http://galaxyproject.org - http://wiki.galaxyproject.org;, and clicking into Learn will likely take to you want to go - the primary hub page for user documentation - including the links in tutorials (plus the wiki side navigation bar with a few different search options). And is true that we do not offer large scale EST to genomic alignment on the public server. Galaxy choices such as BLAST+/Megablast are for use with a local or cloud Galaxy instance. When using a local instance, the tool wrapper can be obtained from the Tool Shed (http://toolshed.g2.bx.psu.edu). A cloud ami would have these tools as part of the package. You can also check the Tool Shed for other options - more are added all the time. Local: http://getgalaxy.org Cloud: http://usegalaxy.org/cloud Hopefully this helps, Jen Galaxy team On 2/2/13 3:17 PM, John Phillips wrote: 1. To Whom it May Concern: I am using the Galaxy interface, and according to the tutorial screencast, I should be able to upload my own reference genome. The address given in the tutorial (http://galaxyproject.org/FTPUpload) leads to a 404 file not found page. I was wondering if there is an alternative site that can allow me to do this. Also, I tried to use the est2genome tool in order to try and align my uploaded sequences. It would only allow me to compare two sequences at a time. Is it possible to align a larger number of sequences at once? I understand there are other programs that allow for this kind of procedure (e.g. Sequencher), but I would like to do this in Galaxy. Thank you for your time, -- -John G. Phillips Graduate Research Assistant University of Tulsa 231-233-6914 ___ 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 Hillman-Jackson Galaxy Support and Training 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/
[galaxy-user] Galaxy Help!!
I am trying to use LEfSe but keep getting the same error. My data loads fine, but then I cannot get results from 'Plot LEfSe Results'. I then try to report the error, but it consistently tells me 'Mail is not configured for this Galaxy instance. So I don't think my error reports are working. Help Please!!! 0 bytes An error occurred running this job:*Traceback (most recent call last): File /usr/local/galaxy-dist/tools/lefse/plot_res.py, line 151, in module else: plot_histo_hor(params['output_file'],params,data,len(data['cls']) == 2) File /usr/local/galaxy-dist/tools/lefse/plot_res.py, li* -- Robert Quinn, Ph.D CFRI Postdoctoral Fellow NLS 301, 5500 Campanile Dr, San Diego State University San Diego, CA, 92182 ___ 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] Galaxy Help!!
Hello Robby, It sounds like you are using the Galaxy instance run by the Huttenhower Lab at Harvard? At this link? http://huttenhower.org/galaxy/ If so, then at the bottom of the home page is a link you can use to contact the lab members about issues with the instance. (They probably have the default bug report email turned off as a preference). Hopefully this puts you in contact with the right folks who can help. Some gentle advice - posting to two public mailing lists at the same time is never a good idea. This was maybe in error? I removed tophat.cuffli...@gmail.com from the cc list. Jen Galaxy team On 7/11/12 4:07 PM, Robby Quinn wrote: I am trying to use LEfSe but keep getting the same error. My data loads fine, but then I cannot get results from 'Plot LEfSe Results'. I then try to report the error, but it consistently tells me 'Mail is not configured for this Galaxy instance. So I don't think my error reports are working. Help Please!!! 0 bytes An error occurred running this job:/Traceback (most recent call last): File /usr/local/galaxy-dist/tools/lefse/plot_res.py, line 151, in module else: plot_histo_hor(params['output_file'],params,data,len(data['cls']) == 2) File /usr/local/galaxy-dist/tools/lefse/plot_res.py, li/ -- Robert Quinn, Ph.D CFRI Postdoctoral Fellow NLS 301, 5500 Campanile Dr, San Diego State University San Diego, CA, 92182 ___ 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://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] Galaxy Help: Extract sequences from [gtf file] + [genome FASTA file]
Edge, Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply. The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract Genomic DNA' tool and set the option 'Interpret features when possible' to Yes. To get sequences for Cufflinks transcripts, use the transcripts.gtf as input to the tool. Best, J. On May 12, 2011, at 3:08 AM, Edge Edge wrote: I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html I'm facing the same problem as well. I'm desired to extract out the assembled transcript by Cufflink. Can I know that how I link my output file from Tophat and Cufflink with the Galaxy? I'm having the following output file right now: junctions.bed insertions.bed deletions.bed accepted_hits.bam human_reference_genome.fasta transcripts.gtf isoforms.fpkm_tracking genes.fpkm_tracking Sorry that I got a bit confusing about the explanation that you given to Karen, in order to get the sequence data for transcripts in a Cuff* GTF file, you'll want to select for only exons (use Galaxy's 'Extract Features' tool) and then use the resultant dataset as input to Extract. Thanks a lot for your advice. best regards edge Master Student UTAR Malaysia ___ 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/
