[galaxy-user] upload more than 2GB data from local computer to local installation of galaxy
Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting for welcome message and after some time ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] upload more than 2GB data from local computer to local installation of galaxy
How can I create ftp for my local computer to upload data for local galaxy installation ? For current I may can use normal text upload but if I am having 10-20 GB file then I will need FTP upload. Waiting for positive reply. Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting for welcome message and after some time Error: Connection timed out Error: Could not connect to server Status: Waiting to retry... Status: Connecting to 127.0.0.1:8080... Status: Connection established, waiting for welcome 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] upload more than 2GB data from local computer to local installation of galaxy
Hi Do, If you are running a loacl instance and you are admin you can use the data library and upload or even better link your data into a data library. https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Cheers, Bjoern Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 http://127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting for welcome message and after some time ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Variant annotation in galaxy
Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history? Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history. Any other suggested tool I can use? Thanks! Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Converting VCF to gd_genotype
I'm interested in using the Genomic Diversity tools. I've used these with success for a previous project. For this current project, I've converted a vcf file (29 subjects) to a gd_genotype file. When I attempt to specify individuals, the checkboxes for each subject are not present. Without specifying individuals, I am unable to complete other analyses (overall FST, etc.) I cannot distinguish a difference between the vcf files that were successful from the previous project and this current project's vcf, but I assume there is a format difference that I cannot detect. I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 22:09:49 2014 (UTC). I can share the histories of the projects if necessary. Mike -- Michael J. Montague, Ph.D. Post-Doctoral Research Associate The Genome Institute, Washington University School of Medicine Forest Park Avenue, Campus Box 8501 St. Louis, MO 63108 T. 718.809.4093 This email message is a private communication. The information transmitted, including attachments, is intended only for the person or entity to which it is addressed and may contain confidential, privileged, and/or proprietary material. Any review, duplication, retransmission, distribution, or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is unauthorized by the sender and is prohibited. If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] upload more than 2GB data from local computer to local installation of galaxy
Hello, Björn is exactly right. Link the data to Galaxy as described on the wiki page he posted. If you want to run FTP server with Galaxy (it is not included by default) you have to install and configure it yourself. Here is a wikipage that will show you how to do it. https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP However if you plan to work with such large files on local machine you might easily end up having to wait for a loong time, depending on what you plan to do with it and what are specifications of the machine. Consider cloud (https://wiki.galaxyproject.org/CloudMan) or public instance ( usegalaxy.org). Martin On Mon, Feb 24, 2014 at 5:30 AM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Do, If you are running a loacl instance and you are admin you can use the data library and upload or even better link your data into a data library. https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Cheers, Bjoern Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting for welcome message and after some time ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Converting VCF to gd_genotype
Hello Mike, Yes, we have similar recent reports of issues with tools from this group and are actively investigating the root cause. It is unknown whether or not python version is related, but right now we are tracking the issues under a single ticket with that as a suspected contributing factor. You can follow this ticket, and any tickets that branch from it, here: https://trello.com/c/yXrDICmg Our apologies for the current inconvenience, Jen Galaxy team On 2/23/14 2:40 PM, Mike Montague wrote: I'm interested in using the Genomic Diversity tools. I've used these with success for a previous project. For this current project, I've converted a vcf file (29 subjects) to a gd_genotype file. When I attempt to specify individuals, the checkboxes for each subject are not present. Without specifying individuals, I am unable to complete other analyses (overall FST, etc.) I cannot distinguish a difference between the vcf files that were successful from the previous project and this current project's vcf, but I assume there is a format difference that I cannot detect. I'm using Galaxy at the main site. I executed the jobs on Fri Feb 21 22:09:49 2014 (UTC). I can share the histories of the projects if necessary. Mike -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Variant annotation in galaxy
Hello Debora, There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org. For the ANNOVAR tool, the supported genome at this time is hg19. When a .vcf file is assigned to that reference genome (aka database), the tool form fills out to display the available annotation to select from. This tool is a brand-new implementation and still undergoing development, so I cannot comment yet about future plans. The best solution is to either run a local Galaxy (with sufficient resources) or what is probably more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrappers for both tools are in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available. The reference data formats can be found on the originating tool sites with supplemental help notes in the Tool Shed repositories. Help to get started is in these links: https://wiki.galaxyproject.org/BigPicture/Choices https://wiki.galaxyproject.org/Tool%20Shed Hopefully one of these solutions will work out you. If there is more to share, we will send a followup reply, Jen Galaxy team On 2/24/14 3:39 AM, garzetti wrote: Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history? Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history. Any other suggested tool I can use? Thanks! Debora ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] large data to upload problem
Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself. As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me. Some option like tell Galaxy about extension and properties of file, so that it should not replicate. By command line 'x' is working fine. Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan doka...@gmail.com ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] large data to upload problem
Hi Do, the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho. Cheers, Bjoern Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself. As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me. Some option like tell Galaxy about extension and properties of file, so that it should not replicate. By command line 'x' is working fine. Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan doka...@gmail.com ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
