Re: [galaxy-user] [galaxy-dev] Welcome.html page
Hi, I've found that I need to be really aggressive with forcing a purge refresh of the browser when changing things like static/welcome.html and static/images/whatever.png. It might be a function of the nginx light-weight HTML renderer within Galaxy caching things on top of the normal caching. You need to purge all the cache in your browswer totally, eg. in Chrome it's Preferences / Delete All Browser Data (or something like that, I'm away from my normal computer). Just forcing a refresah with the usual refresh/reload icon isn't enough. Greg E On Wed, Mar 7, 2012 at 6:52 PM, huayan gao huayan...@gmail.com wrote: Hi Nate, I got a silly question for you. My galaxy is running now but I'd like to customize it. I've changed the welcome.html page but the galaxy mirror site is showing the old one. Do I need to change some other files or other configurations? Also, I add lable in tool_conf.xml file but it does not show up either. Is there another file I need to change too? Best, Huayan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@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/
Re: [galaxy-user] Problems starting Galaxy Cloudman
Also Greg Starting a new cloudman instance with a different cluster name than previously used will always give you a clean environment and setup so you can continue to always use the us-east region. Cheers, Enis On 10/03/2012 2:08 PM, Ross ross.laza...@gmail.com wrote: Since Dannon is likely asleep, maybe this will help until he can respond: http://dev.list.galaxyproject.org/error-on-fastq-file-while-grooming-or-fastqc-report-or-fastqc-converter-td4396664.html ie: try removing the second coverage datatype definition from datatypes_conf.xml and restarting the Galaxy process. On Sat, Mar 10, 2012 at 2:00 PM, Greg Edwards gedwar...@gmail.com wrote: Dannon, Thanks for that. Adding 'migrated_tools_conf.xml.sample' fixed up most problems. I'm left with a couple though. 1. The tools (apart from file upload with Get Data) don't initially execute. This includes my new tools and existing ones like Text Manipulation / Paste Files side-by-side. They stay in the grey waiting to run mode for about 15-30 minutes, then run. 2. When they finally run, they compute and report fine but finish in the Red error colour, and stderr has reported as below.This is both my tools and the system standard ones. WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'coverage', using datatype from /mnt/galaxyData/tmp/tmp6o5hnt. There's an oddity I should mention. When I first fire up galaxy-cloudman-2011-03-22, a remnant of my add-on tools is already showing at the top of the Tools menu. PTM Tools is there, and in tools_conf.xml. But the tools are not in tools/ptmtools, so the menu is inactive. It's like I've corrupted the file systems associated with galaxy-cloudman-2011-03-22. I'm thinking of trying it all on the Singapore AWS node where I can't have touched the AMI's or file sets. This has all been on US East. In fact it's been on US East 1d, I could try on 1a, I never go there normally, but they probably share data. I could try on US West. I'll let you know, if I don't hear before. Greg. On Sat, Mar 10, 2012 at 12:14 AM, Dannon Baker dannonba...@me.com wrote: Greg, The problem here is that the galaxy update failed to merge a change to run.sh because of minor customizations it has. We'll have a long term fix out for this soon, but for now what you can do is ssh in to your instance and update run.sh yourself prior to restarting galaxy. All you need to do is add 'migrated_tools_conf.xml.sample' to the SAMPLES in /mnt/galaxyTools/galaxy-central/run.sh, execute `sh run.sh --run-daemon` (or restart galaxy again from the admin page) and you should be good to go. That new AMI you're seeing is not owned by the Galaxy Team, and we don't actually know who made it. Keep using the same galaxy-cloudman-2011-03-22 for now (and we'll always have the most up-to-date AMI listed at usegalaxy.org/cloud). Because of Cloudman's modular volume design almost nothing resides on the AMI itself, so we can (and do) update the tools and index volumes without having to touch it. So while the AMI reflects a date of almost a year old, the galaxy tools volume (and thus the actual Galaxy instance you're running) has been updated much more recently. One last note- if you're updating and copying your tools in every time, you may want to try using the 'Persist changes' functionality available in the Cloudman admin panel. Once you've set your instance up how you want, if you click 'Persist changes to galaxyTools', it'll create a custom snapshot of your tools volume that will be used from that point forward with this instance. Let me know if you have any more issues, -Dannon On Mar 9, 2012, at 2:53 AM, Greg Edwards wrote: Hi, I'm trying to restart my Galaxy Cloudman service, using the same approach that has been successful over the last couple of months .. - launch AMI 861460482541/galaxy-cloudman-2011-03-22 as m1.large - update from Cloudman console - copy in my tools etc etc - restart - away we go, all works However today the update fails, the log says ... /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.2.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
[galaxy-user] Extracting number of reads from Bowtie analysis
Hello, I am new here! I am aligning Solexa files to genome using tool: NGS: Mapping: Map with Bowtie for Illumina. My question: What is the most easy way to check the number of aligned reads in the output from above? I couldn't find this number directly. I found a way, but it looks circular and unoptimal: to run Bowtie with option: put umapped reads into the file, download the file, open it, count reads, subtract from reads in the original file. However, downloading large files is time-consuming, and I am sure the easier way is somewhere. Further question: good link to help on how to improve number of reads from ChIP study aligned to mouse genome would be also appreciated. best regards, Jerzy ___ 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] Metagenomics
A small warning re-the current cloud-Blast+ config. To properly use the metagenomic tools, if you use the blast+ galaxy tool, make sure to export in blast.XML, then you'll need a script to parse out the readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field contains the correct key to the taxonomy database. Specifically, the Hit_def field is in the format #_#, where the 'gi' id is the first #. The tabular (normal and extended) data does not contain this info. I noticed this after attempting to use the tabular data, and using a trimmed col[1] (supposed to be hit seqID), but my results always came back as a ranked list of the most sequenced genomes in nt basically keying in randomly. j On Wed, Mar 7, 2012 at 4:16 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Vincent, Scott, Filtering raw hits is an important part of a metagenomics analysis pipeline. Please see the methods described in the published metagenomics analysis paper associated with this tool set: Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, and Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. 2009 Nov; 19(11):2144-53. http://www.ncbi.nlm.nih.gov/**pubmed/19819906http://www.ncbi.nlm.nih.gov/pubmed/19819906 Live supplemental data that can be imported and experimented with is available on the public instance, including raw data, working histories, and a tutorial that demonstrates step-by-step the exact methods used in the publication: http://main.g2.bx.psu.edu/u/**aun1/p/windshield-splatterhttp://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter http://main.g2.bx.psu.edu/**library http://main.g2.bx.psu.edu/library- see Windshield splatter Not all tools are available on the public main server, but a local or cloud instance could be used with wrapped tools from the Distribution or Tool Shed, as necessary. For example, BLAST is not available on the public instance, but is included in the distribution for use in local or cloud instances. http://getgalaxy.org Hopefully you will both find this helpful, Jen Galaxy project On 2/29/12 5:32 PM, Montoya, Vincent wrote: Hello I am a relatively new user on Galaxy and I had a question regarding Fetching Taxonomic Information. It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon. For instance, a percentage match. I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match. Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)? Thank you Vincent __**_ 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-devhttp://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/**Supporthttp://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-devhttp://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] Metagenomics
On Mon, Mar 12, 2012 at 6:28 PM, John Major john.e.major...@gmail.com wrote: A small warning re-the current cloud-Blast+ config. To properly use the metagenomic tools, if you use the blast+ galaxy tool, make sure to export in blast.XML, then you'll need a script to parse out the readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field contains the correct key to the taxonomy database. Specifically, the Hit_def field is in the format #_#, where the 'gi' id is the first #. The tabular (normal and extended) data does not contain this info. I noticed this after attempting to use the tabular data, and using a trimmed col[1] (supposed to be hit seqID), but my results always came back as a ranked list of the most sequenced genomes in nt basically keying in randomly. j Hi John, Can you expand on that with a specific example (ideally on the galaxy-dev list, CC'd, since BLAST+ isn't event available on the public galaxy)? Also which version of BLAST+ are you using since I recall some changes to the tabular output IDs prior to 2.2.25 (which is what the wrappers were tested on, I've not tried 2.2.26 yet). Thanks, 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] Metagenomics
Dear GALAXY and Jennifer Although the windshield analysis papers were good starters, They do not address conversed sequence purging or how to get at this information. If anyone has an automated approach I'd be interested . [Discard sequences from blast that have more then 4 hit 99%] Scott Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999- On 3/12/2012 2:28 PM, John Major wrote: A small warning re-the current cloud-Blast+ config. To properly use the metagenomic tools, if you use the blast+ galaxy tool, make sure to export in blast.XML, then you'll need a script to parse out the readID and the Hit_def (as the hit ID). It appears that the 'Hit_def' field contains the correct key to the taxonomy database. Specifically, the Hit_def field is in the format #_#, where the 'gi' id is the first #. The tabular (normal and extended) data does not contain this info. I noticed this after attempting to use the tabular data, and using a trimmed col[1] (supposed to be hit seqID), but my results always came back as a ranked list of the most sequenced genomes in nt basically keying in randomly. j On Wed, Mar 7, 2012 at 4:16 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Vincent, Scott, Filtering raw hits is an important part of a metagenomics analysis pipeline. Please see the methods described in the published metagenomics analysis paper associated with this tool set: Koskovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, and Nekrutenko A. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Research. 2009 Nov; 19(11):2144-53. http://www.ncbi.nlm.nih.gov/pubmed/19819906 Live supplemental data that can be imported and experimented with is available on the public instance, including raw data, working histories, and a tutorial that demonstrates step-by-step the exact methods used in the publication: http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter http://main.g2.bx.psu.edu/library - see Windshield splatter Not all tools are available on the public main server, but a local or cloud instance could be used with wrapped tools from the Distribution or Tool Shed, as necessary. For example, BLAST is not available on the public instance, but is included in the distribution for use in local or cloud instances. http://getgalaxy.org Hopefully you will both find this helpful, Jen Galaxy project On 2/29/12 5:32 PM, Montoya, Vincent wrote: Hello I am a relatively new user on Galaxy and I had a question regarding Fetching Taxonomic Information. It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon. For instance, a percentage match. I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match. Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)? Thank you Vincent ___ 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 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 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 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
[galaxy-user] March 12, 2012 Galaxy Development News Brief
Dear Galaxy Community, The latest Galaxy distributionhas been released: March 12, 2012 Galaxy Development News Brief http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12 *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857 Important Upcoming Changes to Tool Organization: The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *Migrating tools* http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed section of the Galaxy tool shed wiki to understand how this process will work: Migrating tools from the Galaxy distribution to the Galaxy Main tool shed http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed (Summary) In 2012, the Galaxy development team will begin the process of migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distribution_to_the_Galaxy_Main_tool_shed Release Highlights: * Galaxy toolsXML configuration http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_populate_your_Galaxy_tool_panel, managing tool panel layout http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel, and Galaxy tool versions http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions. * RNA-Seq Tools: Added CuffMerge http://cufflinks.cbcb.umd.edu/version 1.0.0, Updated TopHat http://tophat.cbcb.umd.edu/default parameters * External Display Apps: Added *RViewer* http://rviewer.lbl.gov/rviewer, Updated *IGV * http://www.broadinstitute.org/igv/ * Visualize *ENCODE* http://genome.ucsc.edu/ENCODE peak datatype tracks in the Galaxy Track Browser(aka Trackster) * Multiple Workflowupdates including enhancements to/input dataset options, display modes, and sharing * *CloudMan* http://wiki.g2.bx.psu.edu/Admin/Cloud now offers /preliminary support for OpenNebula cloud type http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py/ and a larger /default tools volume/ 10GB vs old 2GB). *Need help with a local instance? * Installation and Admin Instructions: http://getgalaxy.org Searchwith our custom google tools: * All Galaxy mailings lists http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searchingfor prior Q A * Information about deploying, developing, customizing, and administering http://galaxyproject.org/search/getgalaxy Galaxy * Information about using http://galaxyproject.org/search/usegalaxy Galaxy Consider *subscribing to the galaxy-dev* http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing mailing list Thanks for using Galaxy, The Galaxy team --- http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki ___ 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/
