Re: [galaxy-user] New Galaxy User
Gaurav 1. Is there any help file explaining directory structure and what all configuration files used for? The Galaxy wiki is the best place to go for these things, as Louise-Amelie said. You should be able to ignore most things in the config files initially as they will just work. You can ignore most of the directory structure as well, except perhaps the tools directory. 2. I got list of all dependencies from website, Do I have to install all tools in /usr/local/bin/ or can be installed at any custom location? Mostly, the install should (again) just work (install the tarball or distrib and run). I've a got a Galaxy installation checklist here: http://www.agapow.net/science/bioinformatics/galaxy/installing-galaxy It's a bit peculiar to my own situation, but it might give you another point-of-view. Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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] Extract Genomic DNA Problem
Hi, I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server: chr5 4725816847259240 chr181938527 1939965 chr2 101973625 101974007 chr4 7565389875674045 chr194258837 4263299 chr4 3933004939372715 chr4 9606881 9610083 chr157264937 7265599 chr216659189 6667015 chr2 351239 352821 I got the following galaxy output: 7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, chr5 47258168 47259240 Any ideas what I am doing wrong? Thanks, Steve ___ 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 Workshops @ USC June 23-24
Hello all, There will be two Galaxy workshops at the University of Southern California (USC) next week. Both are presented by Jeremy Goecks of Emory University and the Galaxy team. *Both workshops are open to the public:* *Galaxy: A web‐based workbench for interactive and reproducible analysis of high‐throughput sequencing data, Thursday, June 23, 2011* At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health Science Campus, 1450 Biggy Street Registration is free, but required. Register at https://uschsl.qualtrics.com/SE/?SID=SV_bDaxnZwEfrfk1BG 9:15am-Noon Introduction to Galaxy including 30 min. QA Session 2:00pm-5:00pm High‐throughput sequencing data analysis including 45 min. QA Session *Progress and Challenges in Developing a Web-based Platform for Computational Biomedical Research, Friday, June 24, 2011 * See USC ISI AI Seminar Page ( http://ai.isi.edu/index.php?module=seminars/index) for details on time and location. The recent reliance on computation in biology has created an informatics crisis for biomedical researchers: computational resources are often difficult to use, communicating techniques and experiments is challenging, and reproducibility is very limited. Galaxy is one approach for addressing these problems. Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Galaxy provides a collaborative environment for performing complex analyses with automatic and unobtrusive provenance tracking; these features allow transparent sharing of both the precise computational details underlying an analysis and also intent, context, and narrative. Based on experiences with Galaxy, Jeremy will discuss some open problems that might be addressed using artificial intelligence methods and techniques. Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.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] Chip-Seq, Encode Peaks and Galaxy
Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad ___ 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 server issues?
David K Crossman wrote: Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to Get Data and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked Excecute. The 12 moved over to the History panel and after a couple of minutes went from gray to yellow. As of this moment, all 12 are still in the yellow stage (still spinning). Is this normal for that many samples (each sample is about 8GB in size) or should they already have turned green? Any info would be greatly appreciated. Hi David, It's not unlikely for that many files of that size all at once. I've checked the PBS queue and your job is still running. --nate Thanks, David ___ 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/
