Hello. I am trying to set up a copy of Galaxy on my local SuSe Linux machine. I have it running on localhost. I get the following error message when trying to get the genomic sequences for a set of coordinates: "error, format: fasta,database: hg17 Info: Cannot open /depot/data1/cache/alignseq.loc No such file or directory" I'm guessing that the program assumes a certain directory structure to be in place (including a path called /depot/data1/cache). Just wondering if there are other directories I will need to create to get this system running smoothly. I could not find any documentation regarding this on the Galaxy setup page. If such documentation exists, I would be very appreciative if you could point me towards it. Regards. Ryan P.S. Great application nonetheless!
Ryan, Yes certain tools require sequences and alignments stored locally on our own filesystem. These are: sequence extractors genomic score tools ENCODE datasets You don't really want to have those locally as they are truly huge. anton Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu On May 3, 2006, at 2:01 PM, rmorin@bcgsc.ca wrote:
Hello. I am trying to set up a copy of Galaxy on my local SuSe Linux machine. I have it running on localhost. I get the following error message when trying to get the genomic sequences for a set of coordinates:
"error, format: fasta,database: hg17 Info: Cannot open /depot/data1/cache/alignseq.loc No such file or directory"
I'm guessing that the program assumes a certain directory structure to be in place (including a path called /depot/data1/cache). Just wondering if there are other directories I will need to create to get this system running smoothly. I could not find any documentation regarding this on the Galaxy setup page. If such documentation exists, I would be very appreciative if you could point me towards it.
Regards.
Ryan
P.S. Great application nonetheless!
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Ryan, However.... We can study the possibility of making these directories available for download. Or perhaps making an environment variable or something to specific the location of the files so that people can change it easily. Could you tell us a little bit about what you are trying to do, and we can see how we can help. anton Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu On May 3, 2006, at 2:01 PM, rmorin@bcgsc.ca wrote:
Hello. I am trying to set up a copy of Galaxy on my local SuSe Linux machine. I have it running on localhost. I get the following error message when trying to get the genomic sequences for a set of coordinates:
"error, format: fasta,database: hg17 Info: Cannot open /depot/data1/cache/alignseq.loc No such file or directory"
I'm guessing that the program assumes a certain directory structure to be in place (including a path called /depot/data1/cache). Just wondering if there are other directories I will need to create to get this system running smoothly. I could not find any documentation regarding this on the Galaxy setup page. If such documentation exists, I would be very appreciative if you could point me towards it.
Regards.
Ryan
P.S. Great application nonetheless!
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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