[galaxy-user] Question re: Quota not re-setting after data deletion
Hello, I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in order to start fresh, but it still keeps saying my disk is 98% full every though my history has 0 bytes. At the moment, I have nothing in my history, but it is still saying my disk is 98% full. How do I reset the quota to 0 if not by deleting data? Michael R. McGowen, Ph.D. Postdoctoral Research Fellow Molecular Evolution Laboratory Center for Molecular Medicine and Genetics Wayne State University School of Medicine 3240 Scott Hall 540 E. Canfield St. Detroit, MI 48201 USA 313-577-0086 mmcgo...@med.wayne.edu http://homopan.wayne.edu/people/mmcgowen.html ___ 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] Question re: Quota not re-setting after data deletion
Hello Michael, Data will count towards the disk quota when not permanently deleted. Also, once permanently deleted, it will take a bit of time (less than an hour to several hours) for the disk counts in the UI to update. Perhaps this has already been resolved, but if not, hopefully the rest of the advice in this email will help. For details about delete vs delete permanently (and remove from disk), please see: http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently Some things to double check: 1 - Look under Options - Saved Histories to view all histories. Click on Advanced Search, then status: all. Any histories with status active or deleted (in the far right column) may contain data that counts towards the disk quota. Histories with status permanently deleted do not contain any data that counts towards the disk quota. The actual disk usage is in the column Size on Disk. 2 - Look under Options - Histories Shared with Me. Any history shared with you counts towards the disk quota. Copy any data needed and ask for the histories to be unshared. 3 - Check for hidden or deleted (but not permanently deleted) datasets in active histories. Links within each dataset box give the option to permanently delete, which removes them from the disk quota. To do this, from each history, use Options - Show Deleted Datasets and then Options - Show Hidden Datasets to view these. Going through these checks should be quick and it is not uncommon to discover unexpected deleted (but not permanently deleted), hidden, or shared histories data. If after checking you are still having problems, please let us know, Best, Jen Galaxy team On 12/6/11 1:29 PM, Mcgowen, Michael wrote: Hello, I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in order to start fresh, but it still keeps saying my disk is 98% full every though my history has 0 bytes. At the moment, I have nothing in my history, but it is still saying my disk is 98% full. How do I reset the quota to 0 if not by deleting data? Michael R. McGowen, Ph.D. Postdoctoral Research Fellow Molecular Evolution Laboratory Center for Molecular Medicine and Genetics Wayne State University School of Medicine 3240 Scott Hall 540 E. Canfield St. Detroit, MI 48201 USA 313-577-0086 mmcgo...@med.wayne.edu http://homopan.wayne.edu/people/mmcgowen.html ___ 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] Random Intervals ?
Hello Vinny, The tool Text Manipulation - Select random lines from a file may be of interest to you. This will not generate random intervals, but it can select random lines from an interval file or any other file. The ENCODE tool as build specifically on the target genomes using external files. This tool may be generalized at some point in the future, but right now there are no current plans to do so. Hopefully the random line tool will be useful or you will be able to locate an alternative, Best, Jen Galaxy team On 11/29/11 12:43 PM, Vincent Joseph Lynch wrote: To Whom It May Concern, I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the Random Intervals tool within the ENCODE tools? I am using the Aggregate datapoints tool to get phastCons conservation scores for peaks from ChIP-Seq data. I would like to compare these scores to a random expectation so would like to be able to use a Random Intervals-like tool to generate a set of random positions to compare to the experimental set. Best, Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology Yale Systems Biology Institute Yale University There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved. -C. Darwin, 1859 ___ 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/
[galaxy-user] TopHat
Hello Tao, The tools in the group NGS: Picard (beta) - QC/Metrics for sam/bam can generate statistics, in particular the tool SAM/BAM Alignment Summary Metrics. Another choice is NGS: SAM Tools - flagstat. If more statistics are needed, then starting with the original FASTQ and the mapping result SAM file, the tools in Text Manipulation, Filter and Sort, and Join, and Subtract and Group can be used in custom combinations. This question was almost missed. I was able to locate, format, and send as a new thread to the appropriate mailing list. Hopefully this reply helps or you have already found the tools above. Please help us to track new questions and provide prompt help by sending tool and data questions: 1 - to either galaxy-u...@bx.psu.edu or galaxy-...@bx.psu.edu, which are best for most questions. sending to galaxy-b...@bx.psu.edu is mainly reserved for UI bug reports (green bug icon for failed datasets) or for sending shared links to private data. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions 2 - with the to as the mailing list address galaxy-u...@bx.psu.edu. When a brand new question is sent with the mailing list as a cc, it is not tracked. 3 - when a new question is sent as a reply to an earlier thread with a new subject line, it is not tracked. start a new thread for new questions with new subject lines. 4 - please use reply-all if you would like more assistance about the same subject to keep the thread consistent for the user community. Thank you for your help with this! Best, Jen Galaxy team Peng, Tao wrote: Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I find information on how many total reads went into TopHat? How many reads were removed? How many unique hits to reference genome? I was trying to prepare a table for presentation and realize that I could NOT find the information in my GALAXY account? Thanks, tao -- 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/
[galaxy-user] FASTQ Groomer before BWA mapping ?
All, I'm wondering why do we need to convert Illumina FASTQ into sanger using FastQ Groomer before mapping with BWA in galaxy. The lastest version of BWA itself added -I option to use Illumina data directly. What's your opinion on this? Secondly, I found that Map with BWA for Illumina uses -I option in the commandline during execution, even for sanger formatted reads. How does it impact the results? Thanks, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ 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] Genomic interval file for GATK
All, I'm using a locally installed galaxy with GATK 1.3 beta (recently updated). I would be interested in variant calling using GATK on both Illumina and SOLiD data. My questions are: 1) What should be the format that Genomic Interval option can accept in beta version. It produced an error when I provided an (enrichment coords) bed file? DepthOfCoverage had also produced error when I used bed files. Would beta release (v1.3) accept bed file as input for genomic intervals? 2) SAMtool index is seem to be missing in Galaxy. Is this true or any other module (say SAM-BAM) incorporates this functionality? Looking forward to your comments. Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD___ 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/
