[galaxy-user] SNP Calling
Does anyone knows a step-by-step pipeline to SNP calling on illumina dataset? From the alignment to the end thanks Francesco -- ___ 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] Error installing MACS on local Galaxy
Hello, I cannot run MACS on the local Galaxy. When I install MACS version 1.4., it gives error something like cannot find macs. When I install version 1.3.7.1 it gives error /line 34, in module from MACS.OptValidator import opt_validate ImportError: No module named MACS.OptValidator/ I sourced PATH to the directory with this module. Any ideas? best regards, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ 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] How to merge Fastq groomer files in Galaxy?
Dear Galaxy users, Does anyone know how to merge several FASTQ groomer files by using Galaxy? If not, is there any other program that can achieve this? The size of one FASTQ groomer file is around 1GB. Thank you! Best regards, Xiefan Fang, Ph.D. Postdoctoral associate Department of Pediatrics College of Medicine University of Florida Phone: 352-294-5675 Email: xiefanf...@ufl.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] How to merge Fastq groomer files in Galaxy?
On Tue, Oct 16, 2012 at 8:22 PM, Fang,Xiefan xiefanf...@ufl.edu wrote: Dear Galaxy users, Does anyone know how to merge several FASTQ groomer files by using Galaxy? If not, is there any other program that can achieve this? The size of one FASTQ groomer file is around 1GB. Thank you! The Galaxy tool Concatenate datasets tail-to-head under Text Manipulation should work. I'm assuming you just need a simple concatenation of individual FASTQ files, not a more complex merge dealing with duplicates or sorting. Peter ___ 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] FW: problem in data uploading
Hello Amit, Are you using the public Main Galaxy instance at http://main.g2.bx.psu.edu (usegalaxy.org) or another server specific to your project? If you are working with a project's Galaxy server, then you will need to contact the administrator running that instance. It sounds as if you are having trouble loading data into a library (part of your pipeline?). Until loaded successfully, it is expected that tools will not function (#4 below). Please let us know if we can help again, Jen Galaxy team On 10/16/12 2:21 PM, Amit Maiti, PhD wrote: Hi, I am a first time user in galaxy for analysis of my RNA-Seq data. I am facing problem in loading data in galaxy. 1.I successfully transfered fastq files (from Illumina) by FTP and then tried to upload by checking each files and execute. 3. Initially it was yellow (with rotating circle) and then turned pink instead of green. It seems probably there is an error in uploading. But the files disappeared from the upload page but lined up with pink (at the history) and shows that 72.4GB of the disk space are occupied. I can view the files also with ‘display data with viewer’! 4.when I tried analyze with TOPHAT, it tells you have no files in history! 5. When I wanted to do the whole process again but FTP tells yours files are already exists (transferred) in the server. But since they are not at the upload page, I can not upload again each one by checking them to correct the error? 6. Could you please advice me how to solve this problem and successfully upload files that would be good for analysis. Thanks for your help, Amit K. Maiti, PhD Oklahoma medical Research foundation, Oklahoma city, ok 73104 Phone-405 271 8099 Mobile-409 256 9557 ___ 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] cuffdiff values different for same sample
Hello, Thank you for sharing your history. The difference in FPKM values can be explained by the use of the -N option (Perform quartile normalization: Yes). Set this to No to avoid the variable per-run normalization. This has also been discussed at seqanswers.com: http://seqanswers.com/forums/showthread.php?t=4606 Hopefully this helps! Jen Galaxy team On 10/12/12 9:43 AM, i b wrote: Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values as expressed in the output (isoform differential expression). When I ran it again, using a different treated sample, but SAME UNTREATED SAMPLE, the values assigned to the untreated are different. Why is this if values are calculated from a unique FPKM? This happend for other jobs where I have ran the same untreated vs other treated samples... Thanks a lot, ib ___ 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/
[galaxy-user] Export to file
Hi list, Is there a currently a known problem with the export to file function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave ___ 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] cuffcompare input
Hello, Yes, this has not changed. The reference GTF given to Cuffdiff must contain all of the transcripts of the inputs: http://user.list.galaxyproject.org/cuffcompare-inputs-td4654384.html Run this as you have done previously: http://user.list.galaxyproject.org/cuffcompare-outputs-missing-td4654259.html Some other useful advice quoted directly from the tool author: http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge-td4581029.html Hopefully this helps! Jen Galaxy team On 10/17/12 12:34 PM, i b wrote: dear forum, I have two samples, treated and untreated. When I run cuffcompare (to created the gtf file for cuffdiff) do i have to give as input the cufflinks from both samples and the reference annotation or only the treated cuffliks? I very confused. any help much appreciated. thanks, ib ___ 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] Export to file
Hi Dave, Yes, if your Galaxy instance is on the internet, for entire history transfer, you can skip the curl download and just enter the URL from the public Main Galaxy server into your Galaxy directly. To load large data over 2G that is local (datasets, not history archives), you can use the data library option. The idea is to load into a library, then move datasets from libraries into histories as needed. Help is in our wiki here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Take care, Jen Galaxy team On 10/17/12 3:21 PM, Dave Corney wrote: Hi Jen, Thanks for your response and suggestion. Just so that it is clear, for your second method, where I export to file and then use curl, I will download to my computer as an intermediate stage? Is there a simple way to take the history and datasets from PSU galaxy to our Princeton galaxy directly (without downloading to my computer first)? Unfortunately, we don't have FTP on our own galaxy, which is why I was looking for alternatives (each file is 2GB, so uploading through the browser won't work either). It seems that to import from file, the file needs to have a URL and I'm not sure how to go about that if the file is store locally on my computer. Thanks, Dave On Wed, Oct 17, 2012 at 6:12 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Dave, To export larger files, you can use a different method. Open up a terminal window on your computer and type in at the prompt ($): $ curl -0 'file_link' name_the_output Where file_link can be obtained by right-clicking on the disc icon for the dataset and selecting Copy link location. If you are going to import into a local Galaxy, exporting entire histories, or a history comprised of datasets that you have copied/grouped together, may be a quick alternative. From the history panel, use Options (gear icon) - Export to File to generate a link, then use curl again to perform the download. The Import from File function (in the same menu) can be used in your local Galaxy to incorporate the history and the datasets it contains. Hopefully this helps, but please let us know if you have more questions, Jen Galaxy team On 10/17/12 2:37 PM, Dave Corney wrote: Hi list, Is there a currently a known problem with the export to file function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave _ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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 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 -- 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] Export to file
Dave, There's likely something problematic about your history that causing problems. Can you share with me the history that's generating the error? To do so, from the history options menu -- Share/Publish -- Share with a User -- my email address Thanks, J. On Oct 17, 2012, at 6:58 PM, Jennifer Jackson wrote: Hi Dave, Yes, if your Galaxy instance is on the internet, for entire history transfer, you can skip the curl download and just enter the URL from the public Main Galaxy server into your Galaxy directly. To load large data over 2G that is local (datasets, not history archives), you can use the data library option. The idea is to load into a library, then move datasets from libraries into histories as needed. Help is in our wiki here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Take care, Jen Galaxy team On 10/17/12 3:21 PM, Dave Corney wrote: Hi Jen, Thanks for your response and suggestion. Just so that it is clear, for your second method, where I export to file and then use curl, I will download to my computer as an intermediate stage? Is there a simple way to take the history and datasets from PSU galaxy to our Princeton galaxy directly (without downloading to my computer first)? Unfortunately, we don't have FTP on our own galaxy, which is why I was looking for alternatives (each file is 2GB, so uploading through the browser won't work either). It seems that to import from file, the file needs to have a URL and I'm not sure how to go about that if the file is store locally on my computer. Thanks, Dave On Wed, Oct 17, 2012 at 6:12 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Dave, To export larger files, you can use a different method. Open up a terminal window on your computer and type in at the prompt ($): $ curl -0 'file_link' name_the_output Where file_link can be obtained by right-clicking on the disc icon for the dataset and selecting Copy link location. If you are going to import into a local Galaxy, exporting entire histories, or a history comprised of datasets that you have copied/grouped together, may be a quick alternative. From the history panel, use Options (gear icon) - Export to File to generate a link, then use curl again to perform the download. The Import from File function (in the same menu) can be used in your local Galaxy to incorporate the history and the datasets it contains. Hopefully this helps, but please let us know if you have more questions, Jen Galaxy team On 10/17/12 2:37 PM, Dave Corney wrote: Hi list, Is there a currently a known problem with the export to file function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave _ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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 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 -- 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/ ___ 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
[galaxy-user] Can't seem to stop or restart the Galaxy in server
Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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] Can't seem to stop or restart the Galaxy in server
With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it. Hope this helps, Enis On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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] Can't seem to stop or restart the Galaxy in server
Thanks. Helped me! On Thu, Oct 18, 2012 at 11:02 AM, Enis Afgan eaf...@emory.edu wrote: With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it. Hope this helps, Enis On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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/
