Re: [galaxy-user] generic filenames with Export to File
There is currently no way to do this but it would definitely be a useful option to have. I've opened a ticket that you can follow and/or comment on if you're interested: https://bitbucket.org/galaxy/galaxy-central/issue/680/preserve-dataset-names-when-exporting I forgot to mention that you can inspect the datasets_attrs.txt to see the mapping between datasets and files. datasets_attrs.txt contains a JSON dict, so it would be possible to write a little script that renames datasets based on the values in the dict. J.___ 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] Lastz
On Nov 12, 2011, at 6:30 AM, Andrew South wrote: Dear Nate - It seems I may have upset the cluster again: I have 3 Lastz jobs running and cannot upload any more data. I had been uploading fine; started 3 lastz mapping jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP, when I realised I made a mistake, cancelled these jobs, uploaded the correct files and then ran the 3 comparisons (similar files) again and now these jobs have been running 1hr and I cannot upload any more data. Hi Andy, What are the details related to being unable to upload? Are the datasets sitting in a certain state (uploading, queued, etc.)? Did you have any other jobs running at the time? There are some concurrent job limits that could have been responsible. --nate Thanks in advance, Andy Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 17:16 On Nov 11, 2011, at 10:01 AM, Andrew South wrote: Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones will likely queue until free slots are available. Please let us know if there's further trouble, and thanks for using Galaxy, --nate Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 14:55 On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Hi Andy, It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. --nate Thanks, Andy Dr A P South Centre for Oncology and Molecular Medicine University of Dundee Ninewells Hospital Medical School Dundee DD1 9SY Tel 01382 496432 Fax 01382 633952 a.p.so...@dundee.ac.uk Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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 University of Dundee is a registered Scottish charity, No: SC015096 The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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] trimming
Does anyone know if it is possible to trim sequencing adaptor sequences away in Galaxy? and what is the necessary format for trimming sequences? because in Clip adapter sequences I can not to see my files. thaks Diana Trejo, PhD -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] Trouble in extracting species on maf imported from UCSC
Hi Aurelie, The dataset from the UCSC Table browser did not transfer completely, which lead to the other errors. There is a limit to the number of rows of data that can be extracted, to Galaxy or any other type of download. It is around ~100k, but it depends on the data type. The UCSC group would have the details. To access human hg19 MAF data in Galaxy, use these tools, then proceed with the rest of your analysis: - Extract Pairwise MAF blocks given a set of genomic intervals - Extract MAF blocks given a set of genomic intervals Thanks for sending the link and hopefully this option will work for your project, Best, Jen Galaxy team On 11/11/11 4:06 PM, Jennifer Jackson wrote: Hi Aurelie, Would you have time to share a history link containing the two types of datasets for me? Use Options - Share or Publish, generate the link, then email it back to me directly. Please note the dataset(s) with the issue if not obvious (or make a note about it in the info field of the dataset). I will watch for your feedback, Jen Galaxy team On 11/11/11 2:20 PM, 4urelie K wrote: Hi, When I import a multiz46way maf alignement from UCSC, if is is a whole chromosome, then when I try to Filter MAF blocks by Species the list of species does not appear. If I import a small region, it works... Is it a question of size? Although it seems OK when I look at it, could it be a problem in the maf format that I could solve? Thank you, Aurelie ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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] https://galaxy.jgi-psf.org/
On Mon, Nov 14, 2011 at 10:08 PM, Chauhan, Archana achau...@utk.edu wrote: Dear Sir/Madam, I am registered with galaxy http://main.g2.bx.psu.edu/. But I recently came across another link as https://galaxy.jgi-psf.org/ . This has some very good applications especially w.r.t to the genome assembly (MIRA, velvet), microbial ecology (Mothur etc) and Stats/Graphing Tools. Overall this links seems much better than the Main galaxy and fulfils the general aspirations of a user. Is this link subscribed JGI and its collaborators OR any one can be a part of it. Is there any version of galaxy server wherein we can have these applications available for public use. Thank you. Tools like MIRA and Velvet can be extremely demanding to run, so are dangerous/expensive to offer on a public Galaxy. I don't know who exactly runs https://galaxy.jgi-psf.org/ and if they intend it to be available for external usage. I wrote the MIRA wrapper for our in house use with viral genomes (small enough not to be a big computational load) and published it on the Galaxy toolshed for others to use too in their own Galaxy servers. It is nice to see it being used on https://galaxy.jgi-psf.org/ and it looks like they have a pretty powerful cluster with big memory machines with 500GB of RAM, which should cope with many MIRA work loads. If you have a local Galaxy at your department/institute then try asking them if they can install this and other tools of interest for you. Regards, 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/
[galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server
Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukh...@glbrc.wisc.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] enabling regular users to upload large data volumes to a local Galaxy server
FTP server. Ilya -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Yury V Bukhman Sent: Monday, November 14, 2011 3:01 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server Hi, we are running a local Galaxy server, administered by a bioinformatics core group. Our end users increasingly come to us with sets of large NGS files that they can't upload to Galaxy on their own through a web browser. We copy their data to a Galaxy filesystem and upload into data libraries from there using the admin interface. However, the users would prefer to be able get their data onto the server on their own. What's the best solution to that? Should we set up FTP upload? Are there other tricks? Any advice would be appreciated. Thanks. Yury -- Yury V. Bukhman, Ph.D. Associate Scientist, Bioinformatics Group Leader Great Lakes Bioenergy Research Center University of Wisconsin - Madison 445 Henry Mall, Rm. 513 Madison, WI 53706, USA Phone: 608-890-2680 Fax: 608-890-2427 Email: ybukh...@glbrc.wisc.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/ ___ 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/
