[galaxy-user] Deleting a Galaxy User
Dear All, Is it possible to delete a galaxy user or multiple users with a UI call or an API call? Thanks, Oren ___ 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] Question about building a reference genome index using Bowtie
I am trying to compare two genetically different strains that I have sequenced using SOLiD. I was trying to ask where these two strains are different, either in terms of deletions or polymorphisms, and one idea I had was to use Bowtie to create an index from one of these strains and then to map my reads for the other strain using this index. Is this a reasonable strategy? - Will Light Northwestern University ___ 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] Genetrack-Indexer/PeakPredictor
Hi everybody, I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. I still have some questions: 1) Am I correct that the genetrack indexer seems to be down on the Public Galaxy Server? I get a server error, when I start it. (The Genetrack Browser doesn't work either; although I'm still not quite sure whether there are dependencies.) 2) By now, I know one paper on Genetrack - http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I found the following presentation slides: http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy tells me to "cite Blankenberg D, et al. In preparation." Is there additional information? It would be great to know how exactly the peak predictor works, but the slides give only a kind of overview, but of course no explaining and no details and the paper isn't that clear. Thanks, Steffi/ /// ___ 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] Genetrack-Indexer/PeakPredictor
Hi Steffi, GeneTrack should be working again on the Main server, thanks for reporting the error. For information on the inner workings of GeneTrack, you should consult the paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you can additionally contact the GeneTrack author, who I've CC'd here. Thanks for using Galaxy, Dan On Nov 10, 2011, at 11:32 AM, Stefanie Ververs wrote: > Hi everybody, > > I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. > I still have some questions: > > 1) Am I correct that the genetrack indexer seems to be down on the Public > Galaxy Server? I get a server error, when I start it. > (The Genetrack Browser doesn't work either; although I'm still not quite sure > whether there are dependencies.) > > 2) By now, I know one paper on Genetrack - > http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I found > the following presentation slides: > http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy > tells me to "cite Blankenberg D, et al. In preparation." > > Is there additional information? It would be great to know how exactly the > peak predictor works, but the slides give only a kind of overview, but of > course no explaining and no details and the paper isn't that clear. > > Thanks, > > Steffi > ___ > 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/
Re: [galaxy-user] Deleting a Galaxy User
Hi Oren, I am posting the answer given to the galaxy-dev mailing list below for other users, even thought this is a development topic. Next time, please only post to a single mailing list. Thanks! Jen Galaxy team Repost: On Nov 10, 2011, at 11:41 AM, Oren Livne wrote: > Dear Nate, > > Thanks for your answer. > > 1. I could not find it in the admin panel in the UI. When I click on "Manage users", I get the user list and can select users, but there is no "Delete User" button. Hi Oren, Hrm, it looks like the option to delete users was removed from the interface since it couldn't be made conditional on a configuration setting (due to a limitation in Galaxy's "Grids" feature, which is used to display the table of users in the UI). They can be added by uncommented lines 98-100 in lib/galaxy/web/controllers/admin.py: #operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) #operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) #operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) > 2. Which call in the code deletes a user? I can then write my own API method. mark_user_deleted() in lib/galaxy/web/base/controller.py. The preferred method for implementing API methods is by moving the code in the web UI controller which performs the actual action to lib/galaxy/actions/ and then changing the API and UI methods to call that method. See the implementation of the Quota API for a reference. > 3. If I try to reset passwords for more than one user at a time, I get the error trackback: > > TypeError: Odd-length string URL: http://128.135.107.157:8080/admin/reset_user_password > Module weberror.evalexception.middleware:364 in respond view >>> app_iter = self.application(environ, detect_start_response) > Module paste.debug.prints:98 in __call__ view >>> environ, self.app) > Module paste.wsgilib:539 in intercept_output view >>> app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ view >>> return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ view >>> return self.application(environ, start_response) > Module galaxy.web.framework.base:160 in __call__ view >>> body = method( trans, **kwargs ) > Module galaxy.web.framework:173 in decorator view >>> return func( self, trans, *args, **kwargs ) > Module galaxy.web.base.controller:2025 in reset_user_password view >>> user = get_user( trans, user_id ) > Module galaxy.web.base.controller:2413 in get_user view >>> id = trans.security.decode_id( id ) > Module galaxy.web.security:45 in decode_id view >>> return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) > Module encodings.hex_codec:42 in hex_decode view >>> output = binascii.a2b_hex(input) > TypeError: Odd-length string > > 4. A similar problem occurs when I try to delete multiple data libraries under "Manage data libraries". One library deletion works, but multiple yields an error message: > > Invalid Library id ( df7a1f0c02a5b08e,0a248a1f62a0cc04,03501d7626bd192f,3f5830403180d620,2a56795cad3c7db3,417e33144b294c21,5a1cff6882ddb5b2,2d9035b3fc152403,4b187121143038ff,c9468fdb6dc5c5f1,1e8ab44153008be8,e85a3be143d5905b ) specifield. Thanks for reporting these, we'll fix them as soon as possible. I've created a bitbucket here to track them: https://bitbucket.org/galaxy/galaxy-central/issue/678/some-user-and-library-grid-operations --nate On 11/9/11 3:14 PM, Oren Livne wrote: Dear All, Is it possible to delete a galaxy user or multiple users with a UI call or an API call? Thanks, Oren ___ 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
Re: [galaxy-user] Genetrack-Indexer/PeakPredictor
> I think in general you should make sure to cite the authors of the > original publication in addition to Galaxy, the note in Galaxy should > make this explicit. Absolutely agree, the citations are arguably the most important part. The GeneTrack paper citation is currently listed in the help for the tools at http://usegalaxy.org and in -central. Any place where a citation is missing is an error and will be corrected as soon as it is reported. Thanks for using Galaxy, Dan On Nov 10, 2011, at 12:55 PM, Istvan Albert wrote: > Hello Everyone, > >> Galaxy tells me to "cite Blankenberg D, et al. In preparation." > > I think in general you should make sure to cite the authors of the > original publication in addition to Galaxy, the note in Galaxy should > make this explicit. > > Small tidbits that may be useful. There is a command line version for > genetrack with its source code at: > > https://github.com/ialbert/chipexo > > this is a fork of my son's project while he rotated in a lab, he > ported a number of tools including GeneTrack to a command line > interface. Seems to work well but I have not ran it for large genomes. > > In the course that I teach the lectures covering ChipSeq analysis: 19, > 20 and 21 cover the usage and principles of GeneTrack (among other > topics) > > http://bcc.bx.psu.edu/courses/597D-2011/index-597D-2011.html > > best regards, > > Istvan > > > On Thu, Nov 10, 2011 at 12:19 PM, Daniel Blankenberg wrote: >> Hi Steffi, >> GeneTrack should be working again on the Main server, thanks for reporting >> the error. >> For information on the inner workings of GeneTrack, you should consult the >> paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you >> can additionally contact the GeneTrack author, who I've CC'd here. >> >> Thanks for using Galaxy, >> Dan >> >> On Nov 10, 2011, at 11:32 AM, Stefanie Ververs wrote: >> >> Hi everybody, >> >> I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. >> I still have some questions: >> >> 1) Am I correct that the genetrack indexer seems to be down on the Public >> Galaxy Server? I get a server error, when I start it. >> (The Genetrack Browser doesn't work either; although I'm still not quite >> sure whether there are dependencies.) >> >> 2) By now, I know one paper on Genetrack - >> http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I >> found the following presentation slides: >> http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy >> tells me to "cite Blankenberg D, et al. In preparation." >> >> Is there additional information? It would be great to know how exactly the >> peak predictor works, but the slides give only a kind of overview, but of >> course no explaining and no details and the paper isn't that clear. >> >> Thanks, >> >> Steffi >> ___ >> 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/ >> > > > > -- > Istvan Albert > Associate Professor, Bioinformatics > Pennsylvania State University > http://www.personal.psu.edu/iua1/ > ___ 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] Genetrack-Indexer/PeakPredictor
Hello Everyone, > Galaxy tells me to "cite Blankenberg D, et al. In preparation." I think in general you should make sure to cite the authors of the original publication in addition to Galaxy, the note in Galaxy should make this explicit. Small tidbits that may be useful. There is a command line version for genetrack with its source code at: https://github.com/ialbert/chipexo this is a fork of my son's project while he rotated in a lab, he ported a number of tools including GeneTrack to a command line interface. Seems to work well but I have not ran it for large genomes. In the course that I teach the lectures covering ChipSeq analysis: 19, 20 and 21 cover the usage and principles of GeneTrack (among other topics) http://bcc.bx.psu.edu/courses/597D-2011/index-597D-2011.html best regards, Istvan On Thu, Nov 10, 2011 at 12:19 PM, Daniel Blankenberg wrote: > Hi Steffi, > GeneTrack should be working again on the Main server, thanks for reporting > the error. > For information on the inner workings of GeneTrack, you should consult the > paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you > can additionally contact the GeneTrack author, who I've CC'd here. > > Thanks for using Galaxy, > Dan > > On Nov 10, 2011, at 11:32 AM, Stefanie Ververs wrote: > > Hi everybody, > > I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. > I still have some questions: > > 1) Am I correct that the genetrack indexer seems to be down on the Public > Galaxy Server? I get a server error, when I start it. > (The Genetrack Browser doesn't work either; although I'm still not quite > sure whether there are dependencies.) > > 2) By now, I know one paper on Genetrack - > http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I > found the following presentation slides: > http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy > tells me to "cite Blankenberg D, et al. In preparation." > > Is there additional information? It would be great to know how exactly the > peak predictor works, but the slides give only a kind of overview, but of > course no explaining and no details and the paper isn't that clear. > > Thanks, > > Steffi > ___ > 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/ > -- Istvan Albert Associate Professor, Bioinformatics Pennsylvania State University http://www.personal.psu.edu/iua1/ ___ 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] Question about file formats
Hi, I uploaded a bed file to Galaxy and did some text manipulations. I want to download the new file as a bed format that I can then open up in excel or a text editor. However, when I save the data, it is a .tabular format that I cannot open with these programs. What should I do? Thanks, Rena ___ 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 about file formats
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng wrote: > Hi, > I uploaded a bed file to Galaxy and did some text manipulations. I want > to download the new file as a bed format that I can then open up in excel > or a text editor. However, when I save the data, it is a .tabular format that > I cannot open with these programs. What should I do? > > Thanks, > Rena Try renaming the file to end with .tsv or .txt and Excel or your text editor should be happy. 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] my data files are missing from drop down menus
Hello, I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer). The files uploaded successfully and are green in the history section. However, neither file is visible in the drop down menus for any of the tools. I'd appreciate your help with this. Thank you, Maya ___ 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] my data files are missing from drop down menus
Maya,
Many tools require that fastq files specify that they are of sanger quality
score. Specifically, "Map with BWA for Illumina", etc. If you click the
pencil icon ("Edit Attributes") on your uploaded dataset and change the data
type from 'fastq' to 'fastqsanger', you should be able to run your tools.
Thanks, and let me know if you have any other issues.
Dannon
On Nov 10, 2011, at 5:20 PM, Maya Kasowski wrote:
> Hello,
>
> I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer).
> The files uploaded successfully and are green in the history section.
> However, neither file is visible in the drop down menus for any of the
> tools. I'd appreciate your help with this.
>
> Thank you,
> Maya
> ___
> 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/
