[galaxy-user] mount issue
HI, I am getting this when start cluster first time . Error mounting file system '/mnt/galaxyData' from '/dev/sdg3', running command '/bin/mount /dev/sdg3 /mnt/galaxyData' returned code '32' and following stderr: 'mount: you must specify the filesystem type ' Is this a bug ? shd i avoid .. BR Zeeshan ___ 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/
[galaxy-user] /mnt/galaxyIndices/hg19/bwa/base/hg19 not found
Hi, I was following screenshot and after adding workflow http://s3.amazonaws.com/heteroplasmy/heteroplasmy_information.html Upon running it is mentioning that /mnt/galaxyIndices/hg19/bwa/base/hg19 which does not exist .. i have confirmed that after login to instance directly. due to this reason it is unable to pick FASTQ file. any hint ? Also. When we newly create cloud man from AMI dated 22nd March 2011, Does it make sense to update Galxy via admin ? or just run it with out update.. BR Zeeshan ___ 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/
Re: [galaxy-user] Help on installing cutadapt
Hello Tilahun, Are you logged into your Galaxy instance UI using your admin account? This will display the Admin menu. Admin permissions are set up in the universe_wsgi.ini file: # -- Users and Security other items # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://wiki.g2.bx.psu.edu/Admin/Interface #admin_users = None Hopefully this solves the issue. Going forward, you'll probably find that the galaxy-...@bx.psu.edu mailing list is the most helpful for local install questions: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 5/8/12 2:10 PM, Tilahun Abebe wrote: Hi Galaxy users, I tried to install cutadapt for sequence trimming on a local Galaxy instance. I successfully installed Galaxy as an administrator. However, when Galaxy starts, I don't see the administrator option in the top menu bar with the Analyze Data, Workflow, Shared Data, Visualization, Help, and User. It looks like the only way I can install cutadapt is with an administrator option. Any suggestion how I can include the administrator option in the menu? Thanks for your help. Tilahun ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] operate on genomic intervals
Hi Jose, That's great news! A tool tip in the wiki or UI would probably be helpful - your question was a good one. Meanwhile, I'll post your results to back to the list, it may help others who are also working to optimize. Glad that it worked out so well, Jen Galaxy team On 5/8/12 2:57 PM, Xianrong Wong wrote: Thank you Jennifer! I swapped the order of the input datasets which reduced the running time from 2 hrs to 10 min! Jose On Mon, May 7, 2012 at 12:03 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Jose, Very glad to know that you have this working. You question is difficult to address with specificity, as these are completely different algorithms. But in general, any alignment algorithm (Bowtie included) has some sort of indexing strategy (some are better than others) to minimize what is held in memory and process bulk data through. See the Bowtie documentation for how this is achieved. The interval operations tools also have an indexing strategy, specifically, the second input file is the portion loaded memory and the first file is processed against it. So, if you want use an extremely large dataset (or just want to the job to run quicker) try to use it as the first input file if possible. These tools are designed to be used together and with other tools to create workflows, so there should pretty much always be some way to break jobs up (as you did) to get them through the tools, on even modest systems: http://wiki.g2.bx.psu.edu/__Learn/Interval%20Operations http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations Take care, Jen Galaxy team On 5/7/12 8:30 AM, Xianrong Wong wrote: Hello Jennifer, thanks for the advise. It worked when I did it a chromosome at a time. Is there a reason why this is so much more computationally heavy as compared to bowtie? (mapping 190 million reads took only 3-4 hours for me) Jose On Fri, May 4, 2012 at 7:55 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu mailto:j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello Jose, It sounds as if the job is running out of memory. Since you are already working on a cloud, I am going to make the assumption that you have explored the server options with high-capacity memory there. But if not, that is one place to start, in particular your EC2 Instance type, as described on this wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning http://wiki.g2.bx.psu.edu/__Admin/Cloud/CapacityPlanning http://wiki.g2.bx.psu.edu/__Admin/Cloud/CapacityPlanning http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning However, even if that was an option, you may want to consider running your in data through in another way - by running smaller jobs, then merging results, to avoid the large jobs. For example, in the last step where you join to the full BamHI delimited bin file, instead join to groups of bins in that file (perhaps grouped by chromosome), then combine the results to produce the full output. Hopefully this helps provide some options, Jen Galaxy team On 5/4/12 2:18 PM, Xianrong Wong wrote: Hello, I have binned the mouse genome into fragments based on restriction enzyme cut sites. So each bin is a fragment flanked by say BamHI. The output file is in the interval format: chr# start and end coordinates of each bin. I want to count how many times each bin has reads that align to it. I mapped my reads using bowtie and generated a dataset (interval format) for the aligned reads. I then used join in operate on genomic intervals and asked it to return intervals that innerjoin the bin file. The subsequent steps involve grouping and counting and then joining back to the 1st dataset (BamHI delimited bins). I have tried this workflow on small datasets and it worked. However when I subject my full alignment file and full BamHI delimited bin file, the tool fails. I am doing this on cloud. Any advice would be appreciated! Jose _ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on
