Hi Rolando, Please keep all replies on list.
Without a little more information its hard to guess what is happening. Can you provide the log output for when you try to start the server? Is this a cloud instance? If I had to make a guess, it would be that there is a permissions problem due to the copy. Can you make sure that when you copied the .sample file over the .xml file that you did it as the galaxy user? Thanks for using Galaxy, Dan On Nov 13, 2012, at 10:08 PM, rolandomantil...@gmail.com wrote: > I just copy the file datatypes_conf.xml.sample over datatypes_conf.xml like > you told me and now I can't start galaxy it tells me Galaxy deamon not > running,please help > Sent from my Verizon Wireless BlackBerry > From: Daniel Blankenberg <d...@bx.psu.edu> > Date: Tue, 13 Nov 2012 10:10:43 -0500 > To: Rolando Mantilla<rolandomantil...@gmail.com> > Cc: <galaxy-u...@lists.bx.psu.edu> > Subject: Re: [galaxy-user] Warning message > > Hi Rolando, > > You'll need to remove the old blast datatypes from your datatypes_conf.xml > file. If you haven't added any new datatypes manually yourself, you can copy > the datatypes_conf.xml.sample file over of your datatypes_conf.xml file. > > Also, in the future questions about local Galaxy instances should be sent to > the galaxy-dev mailing list. > > > Thanks for using Galaxy, > > Dan > > > On Nov 12, 2012, at 10:31 PM, Rolando Mantilla wrote: > >> I'm having issues with the FASTQ_Groomer. What I have done it first I >> downloaded an SRA file created by an Ion torrent sequencer from the NCBI >> site. Then used the fastq-dump app from the NCBI site to covert the .sra >> file to .fastq file. When I uploaded the data into galaxy it recognized it >> as a fastq(as it should) but when I try to run the FASTQ groomer I get the >> message and warnings below. I also have already downloaded the the >> blast_datatypes tool from the tool_shed. I truly don't know what the issue >> is, any help >> An error occurred running this job: Groomed 12376 sanger reads into sanger >> reads. >> >> WARNING:galaxy.datatypes.registry:Error loading datatype with extension >> 'blastxml': 'module' object has no attribute 'BlastXml' >> WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with >> extension 'blastxml', using datatype from /mnt/galaxyData/tmp/tmpdP_cZ7. >> ___________________________________________________________ >> 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/ >
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