Re: [galaxy-dev] Error Uploading Directory of Files
On Jun 28, 2013, at 12:35 PM, Nicholas Kline wrote: Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed the Galaxy documentation at http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?action=showredirect=Admin%2FData+Libraries%2FUploading+Library+Files to setup this feature: - Admin Data Library Add datasets Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying Job error (click name for more info). Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Hi Nicholas, Could you try re-adding the data to the library with the spaces removed from all path components? I thought this had been fixed a long time ago but it's possible that the bug reappeared at some point. --nate Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: Job error (click name for more info) ? Thank you ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error Uploading Directory of Files
On Mon, Jul 8, 2013 at 3:36 PM, Nicholas Kline nx...@case.edu wrote: Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation ( http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?action=showredirect=Admin%2FData+Libraries%2FUploading+Library+Files ) to setup this feature: - Admin Data Library Add datasets Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying Job error (click name for more info). Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq I have a hunch that the problem could be related to the spaces in the input filename. In this case perhaps the upload.py script is being called without the filename being quoted or escaped. Could you retry from a nice space free import directory? Also does the path where you have installed Galaxy have spaces? Even if Galaxy itself copes, it is highly likely that one or more underlying tools wrapped for use within Galaxy would fail. [I've had minor problems with this with various tools on the Mac outside of Galaxy usage] Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error Uploading Directory of Files
Hi Nicholas, as pointed out by Peter and here: http://www.biostars.org/p/76021/ please check your white spaces and provide a little bit more information. Btw. what is wrong with biostar? Why the double post? Cheers, Bjoern Hi, Our lab recently installed a local version of Galaxy on a mid-2012 Mac Pro computer. We can access the Galaxy server and sign in as an administrator. Today we tried creating a Data Library, adding a dataset to it, and uploading a directory of files. We followed this Galaxy documentation ( http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles?action=showredirect=Admin%2FData+Libraries%2FUploading+Library+Files ) to setup this feature: - Admin Data Library Add datasets Upload directory of files - file format was set to auto-detect - and we chose the option to link to files instead of copying them Galaxy confirmed that the files were successfully uploaded. However, in the data library, under the Message column, is a message in red saying Job error (click name for more info). Clicking on one of the uploaded files displays a page with this information: Date uploaded: 2013-06-28 File size: 7.5 GB Data type: auto Build: sacCer2 Miscellaneous information: Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = Job Standard Error Traceback (most recent call last): File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 386, in __main__() File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 357, in __main__ output_paths = parse_outputs( sys.argv[4:] ) File /Users/administrator/galaxy-dist/tools/data_source/upload.py, line 64, in parse_outputs id, files_path, path = arg.split( ':', 2 ) ValueError: need more than 1 value to unpack error Database/Build: sacCer2 Number of data lines: None Disk file: /Volumes/G-SPEED Q/data/Person 2012 project/DCP2 mef.fastq Questions: 1. Should we be concerned about this error? 2. If so, what is the right way to fix it? 3. If not, how do we remove the red error message next to each file: Job error (click name for more info) ? Thank you ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
