Re: [galaxy-user] problem uploading txt data
Thanks! for fixing the problem before I get time to provide more test data. Chunyu On Tue, May 14, 2013 at 12:17 PM, Daniel Blankenberg wrote: > Hi Chunyu, > > Thanks for reporting this issue, it has been resolved in our stable branch > and will be available on our public server after the next update. > > > Thanks for using Galaxy, > > Dan > > > On May 12, 2013, at 10:52 AM, Chunyu Liu wrote: > > hi, > I had an odd problem today, seems not a problem before: > I am trying to upload a simple tab-delimited text file into galaxy, > but it kept telling me: > empty > format: txt, database: hg19 > The uploaded binary file contains inappropriate content > > Also, showed filesize as 0 bytes. > > I tried Unix format, DOS format. It is a very small data, only 348 bytes. > 4 rows, as attached. > > What is WRONG? > > Thanks! > > Chunyu > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > -- Chunyu Liu, Ph.D. Associate Professor Department of Psychiatry University of Illinois at Chicago ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problem uploading txt data
Hi Chunyu, Thanks for reporting this issue, it has been resolved in our stable branch and will be available on our public server after the next update. Thanks for using Galaxy, Dan On May 12, 2013, at 10:52 AM, Chunyu Liu wrote: > hi, > I had an odd problem today, seems not a problem before: > I am trying to upload a simple tab-delimited text file into galaxy, > but it kept telling me: > empty > format: txt, database: hg19 > The uploaded binary file contains inappropriate content > > Also, showed filesize as 0 bytes. > > I tried Unix format, DOS format. It is a very small data, only 348 bytes. > 4 rows, as attached. > > What is WRONG? > > Thanks! > > Chunyu > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problem uploading txt data
Hi Chunyu, can you provide us with a small, reproducible example? Thanks, Björn > Actually, the file is all tab-delimited, from beginning to end. > It has no problem uploading larger data. Seems to be bug somewhere? > Chunyu > > > On Mon, May 13, 2013 at 12:45 PM, James Taylor > wrote: > Are the first four lines of your file deliberately whitespace? > This > will definitely cause problems for file type detection (it is > not a > valid TSV file as is). > > -- > James Taylor, Assistant Professor, Biology/CS, Emory > University > > > On Sun, May 12, 2013 at 10:52 AM, Chunyu Liu > wrote: > > hi, > > I had an odd problem today, seems not a problem before: > > I am trying to upload a simple tab-delimited text file into > galaxy, > > but it kept telling me: > > empty > > format: txt, database: hg19 > > The uploaded binary file contains inappropriate content > > > > Also, showed filesize as 0 bytes. > > > > I tried Unix format, DOS format. It is a very small data, > only 348 bytes. > > 4 rows, as attached. > > > > What is WRONG? > > > > Thanks! > > > > Chunyu > > > > ___ > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > > > http://galaxyproject.org/search/mailinglists/ > > > > > -- > Chunyu Liu, Ph.D. > Associate Professor > Department of Psychiatry > University of Illinois at Chicago > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problem uploading txt data
Actually, the file is all tab-delimited, from beginning to end. It has no problem uploading larger data. Seems to be bug somewhere? Chunyu On Mon, May 13, 2013 at 12:45 PM, James Taylor wrote: > Are the first four lines of your file deliberately whitespace? This > will definitely cause problems for file type detection (it is not a > valid TSV file as is). > > -- > James Taylor, Assistant Professor, Biology/CS, Emory University > > > On Sun, May 12, 2013 at 10:52 AM, Chunyu Liu wrote: > > hi, > > I had an odd problem today, seems not a problem before: > > I am trying to upload a simple tab-delimited text file into galaxy, > > but it kept telling me: > > empty > > format: txt, database: hg19 > > The uploaded binary file contains inappropriate content > > > > Also, showed filesize as 0 bytes. > > > > I tried Unix format, DOS format. It is a very small data, only 348 bytes. > > 4 rows, as attached. > > > > What is WRONG? > > > > Thanks! > > > > Chunyu > > > > ___ > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > > > http://galaxyproject.org/search/mailinglists/ > -- Chunyu Liu, Ph.D. Associate Professor Department of Psychiatry University of Illinois at Chicago ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problem uploading txt data
Are the first four lines of your file deliberately whitespace? This will definitely cause problems for file type detection (it is not a valid TSV file as is). -- James Taylor, Assistant Professor, Biology/CS, Emory University On Sun, May 12, 2013 at 10:52 AM, Chunyu Liu wrote: > hi, > I had an odd problem today, seems not a problem before: > I am trying to upload a simple tab-delimited text file into galaxy, > but it kept telling me: > empty > format: txt, database: hg19 > The uploaded binary file contains inappropriate content > > Also, showed filesize as 0 bytes. > > I tried Unix format, DOS format. It is a very small data, only 348 bytes. > 4 rows, as attached. > > What is WRONG? > > Thanks! > > Chunyu > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
