I am trying to get a reference genome for drosophila in my local instance of galaxy using the Tool-shed; I installed the data manager successfully, and tried to "run data manager tools"/fetching reference genome; but it did not succeed; looking to the result of my command using "view data manager jobs", I can see that the result of the command:
python /home/patrick/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py "/home/patrick/galaxy-dist/database/files/000/dataset_33.dat" --dbkey_description 'D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)'
There was an error; I asked for the info (i button on the left) and for complete view, and finally, looked the Tool Standard Error (stderr):
Traceback (most recent call last):
File "/home/patrick/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 350, in <module>
if __name__ == "__main__": main()
File "/home/patrick/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 345, in main
REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name )
File "/home/patrick/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 182, in download_from_ucsc
ftp = FTP( UCSC_FTP_SERVER )
File "/usr/lib/python2.7/ftplib.py", line 120, in __init__
self.connect(host)
File "/usr/lib/python2.7/ftplib.py", line 135, in connect
self.sock = socket.create_connection((self.host, self.port), self.timeout)
File "/usr/lib/python2.7/socket.py", line 571, in create_connection
raise err
socket.error: [Errno 111] Connection refused
There was a connexion problem; usually, I got this message when either the address was wrong, or when I could not establish a connexion. My lab is behind a proxy; could it be a port problem and which port must be open ?
Thanks in advance for any help.