May 2012 - galaxy-user - lists.galaxyproject.org

/mnt/galaxyIndices/hg19/bwa/base/hg19 not found
by Zeeshan Ali Shah 11 May '12

11 May '12

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

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Displaying bed files in ucsc
by Xianrong Wong 11 May '12

11 May '12

Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need to convert the file to and where can I do the conversion? Any advise is greatly appreciated! Jose

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mount issue
by Zeeshan Ali Shah 11 May '12

11 May '12

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

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default data for a tool
by alex 10 May '12

10 May '12

Hi, Is there a way to specify default data for a tool, maybe inside an xml? Alex

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Help!!! cuffdiff log2 value
by 杨继文 10 May '12

10 May '12

Hi, I am analyzing my RNA-Seq data. After running cuffdiff, I got a list of differentially expressed transcrpts or genes. As far as I know, log2 value = fold change. However, there are minus values. Is this possible?? log2 value can not be minus. Did I miss something?? Looking forward to your help. Thanks in advance. Best Jiwen

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Re: [galaxy-user] operate on genomic intervals
by Jennifer Jackson 08 May '12

08 May '12

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 <jen(a)bx.psu.edu > <mailto:jen@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 <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu> > <mailto:jen@bx.psu.edu <mailto:jen@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 the public server > at usegalaxy.org <http://usegalaxy.org> > <http://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 > <http://lists.bx.psu.edu/__listinfo/galaxy-dev> > > <http://lists.bx.psu.edu/__listinfo/galaxy-dev > <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 > > > > -- > Jennifer Jackson > http://galaxyproject.org > > -- Jennifer Jackson http://galaxyproject.org

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Help on installing cutadapt
by Tilahun Abebe 08 May '12

08 May '12

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

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Filtering a VCF file
by Laura Reinholdt 07 May '12

07 May '12

I’m using a local instance of Galaxy. I’d like to filter a VCF file for SNPs that have passed filter (as indicated in the VCF file as “PASS” under column 7, FILTER). I can use the basic tab file filter tool (c7==’PASS’), but the resulting file has lost the VCF header and that’s causing a problem with the annotation tool that I want to use. Any advice on how to get around this? Thanks, Laura Laura Reinholdt, PhD Research Scientist Genetic Resource Science The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609-1500 (207) 288-6000, ext. 6693 http://research.jax.org/grs/ http://research.jax.org/faculty/laura-reinholdt.html The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Re: [galaxy-user] operate on genomic intervals
by Jennifer Jackson 07 May '12

07 May '12

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 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 <jen(a)bx.psu.edu > <mailto:jen@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> > > 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 the public server > at usegalaxy.org <http://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 > <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 > > -- Jennifer Jackson http://galaxyproject.org

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operate on genomic intervals
by Xianrong Wong 04 May '12

04 May '12

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

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