Re: [galaxy-dev] Datasets linked into Galaxy do not work
Hi Nate, I found the problem :-). I looked for xsendfile errors in the apache log and that told me that the apache user doesn't seem to have access to the linked datasets, while the galaxy user has. Thanks for pointing me to the interaction between Galaxy and apache. Best regards, Sarah - Ursprüngliche Mail - Von: "Nate Coraor" An: "Sarah Diehl" CC: "galaxy-dev@lists.bx.psu.edu List" Gesendet: Dienstag, 19. Februar 2013 17:59:24 Betreff: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrote: > Hi Nate, > > copied datasets do work and I run Galaxy from the server root. Hi Sarah, I'm having trouble replicating this issue. Could you send along (privately) the relevant portions of your proxy server configuration, and universe_wsgi.ini? Thanks, --nate > > Thanks, > Sarah > > > - Original Message - > From: "Nate Coraor" > To: "Sarah Diehl" > Cc: "galaxy-dev@lists.bx.psu.edu List" > Sent: Wednesday, February 13, 2013 8:22:10 PM > Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work > > On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: > >> Hi all, >> >> I have problems with datasets that were linked into Galaxy data libraries >> (as Admin: "Add datasets", select "Upload files from filesystem paths" and >> "Link to files without copying to Galaxy"). Those files cannot be looked at, >> downloaded or viewed in a genome browser. >> >> Errors in the browser are: >> The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this >> server. >> The requested URL /library_common/download_dataset_from_folder was not found >> on this server. >> An error occurred while accessing: >> http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam >> Read error; BinaryCodec in readmode; streamed file (filename not available) >> >> I don't see any errors in the log files. >> >> We do this kind of linking a lot and everything worked fine in the past. I >> need to use this feature and need it to work, due to hard disk space and >> data duplication. > > Hi Sarah, > > Do display applications work correctly for datasets that were uploaded to a > library and copied in to Galaxy rather than linked? Do you run Galaxy from > the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the > root? > > Thanks, > --nate > >> >> Any help is appreciated. >> >> Best regards, >> Sarah >> ___ >> 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/ > ___ 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/
Re: [galaxy-dev] Datasets linked into Galaxy do not work
On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrote: > Hi Nate, > > copied datasets do work and I run Galaxy from the server root. Hi Sarah, I'm having trouble replicating this issue. Could you send along (privately) the relevant portions of your proxy server configuration, and universe_wsgi.ini? Thanks, --nate > > Thanks, > Sarah > > > - Original Message - > From: "Nate Coraor" > To: "Sarah Diehl" > Cc: "galaxy-dev@lists.bx.psu.edu List" > Sent: Wednesday, February 13, 2013 8:22:10 PM > Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work > > On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: > >> Hi all, >> >> I have problems with datasets that were linked into Galaxy data libraries >> (as Admin: "Add datasets", select "Upload files from filesystem paths" and >> "Link to files without copying to Galaxy"). Those files cannot be looked at, >> downloaded or viewed in a genome browser. >> >> Errors in the browser are: >> The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this >> server. >> The requested URL /library_common/download_dataset_from_folder was not found >> on this server. >> An error occurred while accessing: >> http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam >> Read error; BinaryCodec in readmode; streamed file (filename not available) >> >> I don't see any errors in the log files. >> >> We do this kind of linking a lot and everything worked fine in the past. I >> need to use this feature and need it to work, due to hard disk space and >> data duplication. > > Hi Sarah, > > Do display applications work correctly for datasets that were uploaded to a > library and copied in to Galaxy rather than linked? Do you run Galaxy from > the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the > root? > > Thanks, > --nate > >> >> Any help is appreciated. >> >> Best regards, >> Sarah >> ___ >> 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/ > ___ 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/
Re: [galaxy-dev] Datasets linked into Galaxy do not work
Hi Nate, copied datasets do work and I run Galaxy from the server root. Thanks, Sarah - Original Message - From: "Nate Coraor" To: "Sarah Diehl" Cc: "galaxy-dev@lists.bx.psu.edu List" Sent: Wednesday, February 13, 2013 8:22:10 PM Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: > Hi all, > > I have problems with datasets that were linked into Galaxy data libraries (as > Admin: "Add datasets", select "Upload files from filesystem paths" and "Link > to files without copying to Galaxy"). Those files cannot be looked at, > downloaded or viewed in a genome browser. > > Errors in the browser are: > The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this > server. > The requested URL /library_common/download_dataset_from_folder was not found > on this server. > An error occurred while accessing: > http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam > Read error; BinaryCodec in readmode; streamed file (filename not available) > > I don't see any errors in the log files. > > We do this kind of linking a lot and everything worked fine in the past. I > need to use this feature and need it to work, due to hard disk space and data > duplication. Hi Sarah, Do display applications work correctly for datasets that were uploaded to a library and copied in to Galaxy rather than linked? Do you run Galaxy from the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the root? Thanks, --nate > > Any help is appreciated. > > Best regards, > Sarah > ___ > 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/ ___ 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/
Re: [galaxy-dev] Datasets linked into Galaxy do not work
On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: > Hi all, > > I have problems with datasets that were linked into Galaxy data libraries (as > Admin: "Add datasets", select "Upload files from filesystem paths" and "Link > to files without copying to Galaxy"). Those files cannot be looked at, > downloaded or viewed in a genome browser. > > Errors in the browser are: > The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this > server. > The requested URL /library_common/download_dataset_from_folder was not found > on this server. > An error occurred while accessing: > http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam > Read error; BinaryCodec in readmode; streamed file (filename not available) > > I don't see any errors in the log files. > > We do this kind of linking a lot and everything worked fine in the past. I > need to use this feature and need it to work, due to hard disk space and data > duplication. Hi Sarah, Do display applications work correctly for datasets that were uploaded to a library and copied in to Galaxy rather than linked? Do you run Galaxy from the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the root? Thanks, --nate > > Any help is appreciated. > > Best regards, > Sarah > ___ > 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/ ___ 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/
[galaxy-dev] Datasets linked into Galaxy do not work
Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: "Add datasets", select "Upload files from filesystem paths" and "Link to files without copying to Galaxy"). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Any help is appreciated. Best regards, Sarah ___ 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/
