After multiple restarts of my computer and the galaxy server program, it seems to have come back so I guess that's solved. Still can't successfully fetch reference genomes using the data manager but I guess I should start a new question/thread for that. Gives some dependancy error about samtools but I'm not sure if that is the real issue stopping it. Anyway, thanks. Stephen Date: Tue, 10 Jun 2014 10:39:55 -0400 Subject: Re: [galaxy-dev] Missing navigation pane From: dannon.baker@gmail.com To: sedwards_28@hotmail.com CC: galaxy-dev@bx.psu.edu Hey Stephen, Can you look in the server logs to see if there are any errors being reported? Or if there are any javascript errors in the browser window? You may also want to try clearing your browser cache. -Dannon On Tue, Jun 10, 2014 at 1:54 AM, Stephen E <sedwards_28@hotmail.com> wrote: I installed a local instance of galaxy approximately a month ago (build 2014.04.14). I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem. I ran "hg pull" and then "hg update latest_2014.06.02". I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade). When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it. How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending "/admin" to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking. ___________________________________________________________ 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/

Hi Stephen, Can you provide the error message from the job? You can look at bug-report for the the output dataset created by the data manager for the “Data Manager History (automatically created)” history in your saved histories. Also any other relevant information from the log would be great as well. Thanks for using Galaxy, Dan On Jun 12, 2014, at 8:24 PM, Stephen E <sedwards_28@hotmail.com> wrote:

I installed a local instance of galaxy approximately a month ago (build 2014.04.14) and have since updated to latest_2014.06.02. It is running on 64-bit Ubuntu 12.04.

I'm having an issue with the Data Manager to fetch reference genomes (data_manager_fetch_genome_all_fasta, Rev. 2ebc856bce29). It will successfully submit a job to the queue but it quickly has an error. I'm selecting UCSC as the source and bosTau7 as UCSC's DBKEY for source FASTA.

The only error/warning I see in the server logs seems related to samtools: galaxy.tools.deps DEBUG 2014-06-12 20:07:30,952 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-06-12 20:07:30,952 Failed to resolve dependency on 'samtools', ignoring

Samtools 0.1.19 seems to be installed through galaxy and I also installed samtools through apt-get. I installed the apt-get version after the first time trying this didn't work.

In the list of jobs, it has an error state and the command line is the following: python /home/stephen/Work/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/stephen/Work/galaxy-dist/database/files/000/dataset_22.dat" --dbkey_description 'unspecified (?)'

I need to use the bosTau7 (or perhaps bosTau6) cow reference genomes and can't figure out any other ways to properly load them into galaxy. I'd like them available for everything on the server and would prefer this over using a custom reference genome. I may be missing something obvious because the command line doesn't seem to specify the genome I want but I can't type anything new into the "DBKEY to assign data" field.

How can I get the fetch genome data manager to work or otherwise load the bosTau7 reference genome into galaxy?

Thanks,

Stephen ___________________________________________________________ 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/

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