Re: [galaxy-dev] Problem uploading files from filesystem paths
Hello, I set the library_import_dir setting in my universe_wsgi.ini file so that I could upload a directory of files into galaxy. I'm getting the following error screen when I attempt the upload from /tmp. The permissions are that galaxy owns the files in /tmp. I get the same error message when I try to upload the files from my computer. -rw-r--r-- 1 galaxy stapusr 656960285 Apr 10 14:36 117681r.bam Uploaded by:re...@channing.harvard.edu Date uploaded:2012-04-10 File size:626.5 Mb Data type:auto Build:? Miscellaneous information:uploaded bam fileTraceback (most recent call last): File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 410, in __main__() File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 399, in __main__ Job Standard Error Traceback (most recent call last): File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 410, in __main__() File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 399, in __main__ add_file( dataset, registry, json_file, output_path ) File /share/shared/galaxy-central-hbc/tools/data_source/upload.py, line 338, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File /share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /share/shared/galaxy-central-hbc/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/local/python27/lib/python2.7/subprocess.py, line 672, in __init__ errread, errwrite) File /usr/local/python27/lib/python2.7/subprocess.py, line 1202, in _execute_child raise child_exception OSError: [Errno 13] Permission denied error Database/Build:? Number of data lines:None Disk file:/share/shared/galaxy-central-hbc/database/files/000/dataset_40.dat ___ 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] Problem uploading files from filesystem paths
Seems like an error concerning permissions in your galaxy folders. Try: sudo chmod 777 galaxy-dist/ and then try to upload data again. To: galaxy-...@bx.psu.edu From: liisa.ko...@dnalandmarks.ca Date: Tue, 20 Dec 2011 16:22:02 -0500 Subject: [galaxy-dev] Problem uploading files from filesystem paths Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas? Thanks in advance, Liisa Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/lib64/python2.6/subprocess.py, line 633, in __init__ errread, errwrite) File /usr/lib64/python2.6/subprocess.py, line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied ___ 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] Problem uploading files from filesystem paths
Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas? Thanks in advance, Liisa Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/lib64/python2.6/subprocess.py, line 633, in __init__ errread, errwrite) File /usr/lib64/python2.6/subprocess.py, line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied ___ 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/
