- galaxy-user - lists.galaxyproject.org

Extract genomic DNA-strand information is not recognized
by Sarah 26 Oct '11

26 Oct '11

Hello, I am trying to extract sequences from a FASTA file containing genomic information. The coordinates are in a tab-delimited format, which is recognized as BED format by Galaxy (meaning that the 6th column is correctly interpreted as 6. Strand). However, upon running "Fetch sequences" , Extract Genomic DNA only the +-strand information is included in the output FASTA file and I receive the following ERROR message: 1,431 sequences format: fasta, database: ? Info: 1476 warnings, 1st is: Invalid interval, start '1616' > end '1177'. Skipped 1476 invalid lines, 1st is #2, "scaffold00001 1616 1177 Fom - 1" Is this a bug? How can I can adjust my input data files to get the --strand sequences as well? I have seen a similar problem in an earlier posting and there it was suggested to manually adjust the strand information column 5, but this did not work for me neither. Many thanks for your all help!!!!! Sarah

2 1

Allelic RNA-seq!
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hello Di, I am posting to the mailing list (as you intended?). Regards, Jen Galaxy team On 10/25/11 1:51 PM, Di Nguyen wrote: > Hi Jen, > > May I ask you and the community this question: > > I am sequencing the transcriptome of a hybrid mouse (BL6 x spretus). The > reference BL6 is available but Mus spretus' is not, even though the SNPs > table for spretus is available. How do I use Galaxy to identify > species-specific transcripts? > > Please accept my utmost appreciation, > > Di > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

1 0

Re: [galaxy-user] Reducing overall data footprint
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hi Bryn, Removing unneeded data is the best solution if using Main. One example would be saving back (locally) the original FASTQ input, then deleting it permanently from your history, rather than leaving both the raw data and the Groomed data on the server. This can actually help quite a bit if your datasets are large. See this wiki for help about Delete vs Delete Permanently: http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions Another option is to move to a local or cloud instance: http://getgalaxy.org I am posting back to the mailing list along with a clearer subject line, to help others who may have a similar question. Best, Jen Galaxy team On 10/25/11 10:54 AM, Bryn Gaertner wrote: > Hi Jennifer, > > I am trying to run cufflinks, which I don't > think should be too hard (it's on C. elegans). Do you have any > suggestions for reducing the amount of memory I'm sucking? > > Thanks! > Bryn -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

1 0

Re: [galaxy-user] data sizes & delete vs delete permanently
by Jennifer Jackson 25 Oct '11

25 Oct '11

Hi Richard, How to know overall size: Your total size is in the very upper right corner, in a lavender box. This is also noted when using the link "User -> Preferences" from the top menu bar. The size of an individual history is noted in the right history panel, located underneath the "Options" pull-down menu. How to delete permanently: Please see the wiki about Managing Datasets at: http://galaxyproject.org/wiki/Learn/Managing Datasets#Actions Specifically, the section about Delete vs Delete Permanently, although tips for moving data around are throughout the document. In short: if you just delete, the data is recoverable (by you), and it still counts as part of your quota. If you delete permanently, then it is not recoverable (by anyone, including admins), and is removed from your quota. It is probably worth the time to copy/export/save back anything to may miss when first testing out the "delete permanently" functions for individual datasets and complete histories. Hopefully this helps. I am posting back to galaxy-user(a)bx.psu.edu for others that may need similar help. All of this is in the wiki, but more detail (graphics, etc.) is planned for in the near-term to clarify the functions further. Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

1 0

Galaxy Main public instance: data and job quotas
by Jennifer Jackson 25 Oct '11

25 Oct '11

Galaxy Main public instance: data and job quotas October 25, 2011 Dear Galaxy User, Thank you very much for using our free and open public resource. Galaxy has become extremely popular and as a result many people rely on it daily for their analysis needs. Previously our service had no restrictions on usage, which is not sustainable in the long term. To continue providing our open service in a fair manner, we are now implementing quotas at the public Galaxy Main instance http://usegalaxy.org (http://main.g2.bx.psu.edu) The Main quotas are: Data - 250Gb for registered users (with a Galaxy account) - 5Gb for unregistered users Jobs - 8 concurrent jobs running simultaneously (all users) For more details please see: Galaxy Main Wiki http://galaxyproject.org/wiki/Main Data management: accounting and disk quotas http://galaxyproject.org/wiki/Admin/Disk%20Quotas Managing Datasets in Galaxy http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions For those users with current account disk usage over the quota limit, we will be implementing a step-down program over the next several weeks. Details for that program will be emailed to those users directly. If you find that you require additional resources, please consider the alternative Galaxy options: http://galaxyproject.org/wiki/Big%20Picture/Choices Thanks for using Galaxy! -- The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org

1 0

Re: [galaxy-user] Permissions and private roles
by Greg Von Kuster 25 Oct '11

25 Oct '11

Hello Anthony, On Oct 24, 2011, at 10:01 AM, Anthony Underwood wrote: > Hi Greg > > Thanks for the reply. I can see now that as an admin user I can now add private roles using the Admin View as opposed to the data libraries view. > It is still a bit unclear how a folder can be visible to one user but not to another. If both users have access to the library then they can view all folders, correct? Permissions on a folder are derived from permissions on specific datasets contained in the folder. So, if folder1 contains dataset1 and dataset2, and only Jack can see dataset 1 in folder1 and only Jill can see dataset2 in Folder1, both Jack and Jill can see Folder1, but Spot cannot. In addition, even though both Jack and Jill can see Folder1, each of them will be able to see only their respective dataset. > I can see how I can edit add/modify permissions for a folder but not the view/access permission. > > Also another question about permissions. If I create a Galaxy page and share that with limited users then it appears that the datasets are all public via a URL is that correct? I'm not the expert on pages, Jeremy, can you answer this one? > > Thanks again > > Anthony > > > On 24/10/2011 14:09, "Greg Von Kuster" <greg(a)bx.psu.edu> wrote: > >> Hello Anthony, >> >> On Oct 24, 2011, at 6:55 AM, Anthony Underwood wrote: >> >>> Permissions and private roles >>> Hi all >>> >>> I’m trying to get my head round permissions on Data Libraries. I have a couple of questions >>> 1) When I come to give access to a library the only roles I see are the current (admin) user’s private roles and other non-private roles I have created - no other private roles. >> >> The list of roles you see on the permission page for data library items ( folders and datasets ) is dependent upon the following: >> >> 1. Whether you are setting permissions on the library item from the Admin view ( where you should see both private and public roles ) or the Data Libraries view ( where you should only see your own private roles along with certain other public roles >> >> 2. The level in the hierarchy of the data library at which you are setting permissions. At the top level ( the data library level ), you have the ability to set the LIBRARY_ACCESS permission for the entire data library hierarchy. Depending upon the roles you associate here, all lower levels in the data library hierarchy show only those roles that are derived from the roles you set at the top LIBRARY_ACCESS permission. This is because it makes no sense to allow user john to have some permission to do something in a lower folder of a data library when he is not associated with the permission to even access the library at the top level. >> >>> Reading the wiki page suggests that I should see all roles private and non-private. >> >> Not knowing which wiki you've read, make sure to see these: >> >> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Library%20Security >> >> http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFile&do=get&target=GD… >> >>> 2) Is there a way to give a role access to just one folder of a library rather than the whole library? >> >> Yes, but again, the user with the role must be able to access the data library ( either the data library is public, or the user with the role is associated with the LIBRARY_ACCESS permission at the top level. >> >> >>> >>> Many thanks >>> >>> Anthony >>> Dr Anthony Underwood >>> Bioinformatics Group | Applied Laboratory and Bio- Informatics Unit >>> Microbiology Services, Colindale >>> 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 <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/ >> >> Greg Von Kuster >> Galaxy Development Team >> greg(a)bx.psu.edu >> >> >> >> > > > > ************************************************************************** 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 ************************************************************************** Greg Von Kuster Galaxy Development Team greg(a)bx.psu.edu

3 6

Permissions and private roles
by Anthony Underwood 24 Oct '11

24 Oct '11

Hi all I¹m trying to get my head round permissions on Data Libraries. I have a couple of questions 1) When I come to give access to a library the only roles I see are the current (admin) user¹s private roles and other non-private roles I have created - no other private roles. Reading the wiki page suggests that I should see all roles private and non-private. 2) Is there a way to give a role access to just one folder of a library rather than the whole library? Many thanks Anthony Dr Anthony Underwood Bioinformatics Group | Applied Laboratory and Bio- Informatics Unit Microbiology Services, Colindale 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 **************************************************************************

2 2

tool.xml "&>" console redirection within command-tag
by Appelt, Uwe 24 Oct '11

24 Oct '11

Dear all, that has probably been asked 10e6 times, however, I don't find any comments on how to properly escape special characters in a toolxy.xml. What I want to achieve is the following: <command interpreter="bash">$myScript &> $logFile</command> where myScript is dynamically created (as part of the configfiles-section) and the logFile is where stderr and stdout should go to. Now the problem is obviously the "&"-character, because it causes the following error-msg on reloading the toolxy.xml: ExpatError: not well-formed (invalid token): line 5, column 50 where the 5/50 refers to the "&"-character. By the way: redirecting either stdout or stderr by specifying just ">" (instead of "&>") works fine. I tried a lot of different notations in the meanwhile, but neither something like "\&>" nor "\&>" works. Any suggestions? Many thanks in advance and Cheers! Uwe

2 6

Permissions and private roles
by Anthony Underwood 24 Oct '11

24 Oct '11

Hi all I¹m trying to get my head round permissions on Data Libraries. I have a couple of questions 1) When I come to give access to a library the only roles I see are the current (admin) user¹s private roles and other non-private roles I have created - no other private roles. Reading the wiki page suggests that I should see all roles private and non-private. 2) Is there a way to give a role access to just one folder of a library rather than the whole library? Many thanks Anthony Dr Anthony Underwood Bioinformatics Group | Applied Laboratory and Bio- Informatics Unit Microbiology Services, Colindale Health Protection Agency 61 Colindale Avenue London NW9 5EQ t: 0208 3276466 f: 0208 3277404 e:anthony.underwood@hpa.org.uk ----------------------------------------- ************************************************************************** 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 **************************************************************************

1 0

analysis of 454 data
by bassanio 24 Oct '11

24 Oct '11

Dear All, I'm very very much new to this ngs platform... and I'm currently getting started to work with ngs analysis as first assignment i had got raw sequence out of 454 and that too multiplexed. I had got couple of fna and qual files. only thing i know is that this is of bacterial genome. I like to know what type of analysis i can do with this and how.. i clearly know this is a wide question but do please help me out to get started and pls find time to give me an outline to start with -- ~~~~Auf Wiedersehen~~~~ Liebe

2 3