[galaxy-user] Cannot upload file to data library
Hi all, I created an account in our local Galaxy instance and it's a non-admin one. I have set up Galaxy (I have an account that's an admin) so that my user account can upload files to a data library. But when I tried doing it, I got the following error: The directory some folder here contains no valid files. I checked the path to the folder and it was correct. I also checked if I had really placed the FASTQ file inside the folder and I found the file there. Why is Galaxy telling me that there is no valid file within the folder when there's a file present within the directory? Thank you in advance for any help! CL ___ 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] Problem with Depth of Coverage on BAM files (GATK tools)
Hi Lilach, Sorry for the late response. Jen just confirmed the disadvantages of my approach. I don't know how difficult could be for you to double check the coordinates you have in your interval file are correct for hg_g1k_v37. If you feel confident they will work and want to proceed, you could do something like this outside of galaxy, you could also I'm sure find a way to do it inside galaxy: sed 's/^chr//' interval_file.csv interval_file_g1k.csv If you have coordinates for the mitochondrial chromosome you might have to do also: sed 's/^MT/M/' interval_file.csv interval_file_g1k.csv As if I remember correctly UCSC uses chrMT and GATK expects just M. Please double check this as I'm not sure. It would be also nice is there were a confirmation on what exactly hg_g1k_v37 is, and where you could find annotations for it. Annotations from Ensembl would do? Regards, Carlos On Mon, Jun 25, 2012 at 5:22 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Lilach, Currently, the human reference genome indexed for the GATK-beta tools is 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so we expect there to be little to no change to the beta version on the main public instance until this is completed. Attempting to convert data between different builds is not recommended. These tools are very sensitive to exact inputs, which extends to naming conventions, etc. The best practice path is to start and continue an analysis project with the same exact genome build throughout. If you want to use the hg19 indexes provided by the GATK project, a cloud instance is the current option (using a hg19 genome as a 'custom genome' will exceed the processing limits available on the public Galaxy instance). Following the links on the GATK tools can provide more information about sources, including links on the GATK web site which will note the exact contents of the both of these genome versions, downloads, and other resources. Hopefully this helps to clear up any confusion, Best, Jen Galaxy team On 6/21/12 7:50 AM, Lilach Friedman wrote: Hi Jennifer, Thank you for this reply. I made a new BWA file, this time using the hg19(full) genome. However, when I am trying to use DepthOfCoverage, the reference genomr is stucked on the hg_g1k_v37 (this is the only option to select), and I cannot change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the previous time I tried to use DepthOfCoverage. It seems as a bug? How can I change it? Thanks, Lilach 2012/6/18 Jennifer Jackson j...@bx.psu.edu Hi Lilach, The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run. UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 with UCSC hg19 for an explanation. Reference genomes must be exact in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. Good luck with the re-run! Jen Galaxy team On 6/18/12 4:42 AM, Lilach Friedman wrote: Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main # ERROR -- # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): # ERROR The invalid argume Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach ___ The Galaxy User
[galaxy-user] Converting to index files of viral genome for running TopHAT
I was wondering if it is some how possible in galaxy to format FAST genome seq file of microbial genome to format to generate bowtie index so that it can be used for RNA seq analysis using TopHat. Alternatively any pointer to an available tool which can generate index files. Thanks Kanwar ___ 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] Converting to index files of viral genome for running TopHAT
Hello Kanwar, If you want to use a microbial genome, it can be used as a custom reference genome in Galaxy the same as any other reference genome, with Bowtie or TopHat. Instructions are at this wiki: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome To index the data and use in a local instance, you will want to create the indexes on the command line. Follow the instructions in our admin wiki: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup The above are technical set-up. There are still scientific considerations. Reviewing the RNA-seq pipeline's manuals, researching Q/A on message boards such as seqanswers.com, and perhaps contacting the tool authors would be strongly recommended to determine if this is the appropriate tool set for your purposes: http://tophat.cbcb.umd.edu/ http://cufflinks.cbcb.umd.edu/ tophat.cuffli...@gmail.com Best, Jen Galaxy team On 6/26/12 7:36 AM, shamsher jagat wrote: I was wondering if it is some how possible in galaxy to format FAST genome seq file of microbial genome to format to generate bowtie index so that it can be used for RNA seq analysis using TopHat. Alternatively any pointer to an available tool which can generate index files. Thanks Kanwar ___ 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] How to revive my account that had been marked as deleted?
Dear all, Has any one encounter this situation that the public galaxy server sent back this message as I tried to log in my account, This account has been marked deleted, contact your Galaxy administrator to restore the account. How can I deal with this problem? I thought it was possible that I had run more than 8 jobs concurrently, so the server automatically deleted my account. How do I revive my account, and any one know what is the galaxy administrator's email? I thanks a lot in advance. Pathomida ___ 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] Quick question about cuff compare
Hi! Just a quick question I am trying to use cuffcompare for human data and want to use a Sequence Data (h19). I can only seem to find the fasta files divided by chromosome. If I upload all of these files individually will the program be able to simultaneously use the files (it looks as though there is only space to input 1 file...)? Or do I need to find the whole genome in 1 Sequence Data file? Thanks in advance for your help! Kind Regards, Jason ___ 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] Quick question about cuff compare
Hello Jason, Are you using the public main Galaxy instance at http://main.g2.bx.psu.edu (usegalaxy.org)? The hg19 database can be used as a locally cached reference genome with the Cuff* RNA-seq tools, so there isn't any need to load external fasta files. If you do decide to use a custom genome in the future (a different genome), individual chromosomes can be merged with the tool Text Manipulation - Concatenate datasets. More help with format is on our wiki: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Thanks, Jen Galaxy team On 6/26/12 8:50 AM, Jason Serviss wrote: Hi! Just a quick question I am trying to use cuffcompare for human data and want to use a Sequence Data (h19). I can only seem to find the fasta files divided by chromosome. If I upload all of these files individually will the program be able to simultaneously use the files (it looks as though there is only space to input 1 file...)? Or do I need to find the whole genome in 1 Sequence Data file? Thanks in advance for your help! Kind Regards, Jason ___ 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] Complete Genomics CGA Tools™� in Galaxy
Dear Community Members Complete Genomics, Inchttp://www.completegenomics.com/. is happy to announce the release of a CGA Tools™ implementation in Galaxy. CGA Tools™ is an open source projecthttp://cgatools.sourceforge.net/ to provide tools for downstream analysis of Complete Genomics Whole Genome Sequencing data. This first release includes the most commonly used functions of CGA Tools™ such as listvariants, testvariants, calldiff, snpdiff, junctiondiff, join and varfilter. Ongoing development will add other functions of CGA Tools™, which were not part of this release, and a variety of data analysis workflows. There are two repositories available for download from the Galaxy Tools Shedhttp://toolshed.g2.bx.psu.edu/: a linux version, cg_cgatools_linux, and a Mac OSX version, cg_cgatools_mac_osx. Both repositories are bundled with the latest version of CGA Tools™ (1.5.0.31) for the respective operating system and contain instructions for automated and manual installation of the tools, as well as instructions for the download and installation of reference genome files. Please reply to this post with any comments to this release and suggestions for future development, or contact us at profs...@completegenomics.commailto:profs...@completegenomics.com Best regards Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. The contents of this e-mail and any attachments are confidential and only for use by the intended recipient. Any unauthorized use, distribution or copying of this message is strictly prohibited. If you are not the intended recipient please inform the sender immediately by reply e-mail and delete this message from your system. Thank you for your co-operation. ___ 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] Quick question about cuff compare
Hello Jason, The short answer is that the database is interpreted from the database assignment of the inputs to the tool. Have you seen our RNA-seq tutorial? It may answer some of the other questions. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Best, Jen Galaxy team On 6/26/12 2:02 PM, Jason Serviss wrote: Hello Jennifer, Thank you for your prompt reply! Yes, I am using the public main Galaxy at the link you included. So just to clarify (sorry its my first time doing this), if I select locally cached the analysis will automatically be done with a Sequence Data file located on the server? How is the proper species Sequence Data selected (i.e. h19 in this case) and the version? I didn't receive a prompt to select any specific database after clicking the locally cached option. Do I need to place h19 in my history? I looked in Galaxy for a link to Cuff*RNA-seq tools (which you had mentioned), but couldn't manage to locate it... Thanks for your patience! Kind Regards, Jason 2012/6/26, Jennifer Jackson j...@bx.psu.edu: Hello Jason, Are you using the public main Galaxy instance at http://main.g2.bx.psu.edu (usegalaxy.org)? The hg19 database can be used as a locally cached reference genome with the Cuff* RNA-seq tools, so there isn't any need to load external fasta files. If you do decide to use a custom genome in the future (a different genome), individual chromosomes can be merged with the tool Text Manipulation - Concatenate datasets. More help with format is on our wiki: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome Thanks, Jen Galaxy team On 6/26/12 8:50 AM, Jason Serviss wrote: Hi! Just a quick question I am trying to use cuffcompare for human data and want to use a Sequence Data (h19). I can only seem to find the fasta files divided by chromosome. If I upload all of these files individually will the program be able to simultaneously use the files (it looks as though there is only space to input 1 file...)? Or do I need to find the whole genome in 1 Sequence Data file? Thanks in advance for your help! Kind Regards, Jason ___ 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 -- 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/
