- galaxy-user - lists.galaxyproject.org

taxBuilder executable
by Edward Kirton 06 Feb '10

06 Feb '10

taxonomy/gi2taxonomy.py gives me this error: /bin/sh: taxBuilder: command not found what is this taxBuilder program and where do i find it? i didn't find anything via google thanks!

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Re: [galaxy-user] Question from UCSC about SNPs and proteins
by Guruprasad Ananda 02 Feb '10

02 Feb '10

Hi Jen, "Mutate Codons with SNPs" tool under "Evolution" section on Galaxy should help to answer this question. If you look at the tool's help section, it explains the required format of the input dataset. The input should have start, end, stop and strand co-ordinates for each of the codons, joined with start, end, stop, strand co-ordinates and observed SNPs for each of the SNPs. If the user has these data in two separate files, he can join them using "Join" tool under "Operate on genomic intervals" section. The output of the tool will consist of codons in the input mutated with the respective SNPs. To check if the changes are synonymous or not, the user can join this output with a tabular file containing the genetic code using "Join two queries" tool under "Join, subtract and group" section. I hope this answers your questions. Please feel free to email us if you have any further queries. Also, please send any future Galaxy-related questions to our mailing list at galaxy-user(a)bx.psu.edu. Thanks! Guru Galaxy team. On Jan 29, 2010, at 7:54 PM, Jennifer Jackson wrote: > Hi Guru, > > We have a question that we do not have a straightforward answer to. After reviewing the tools at Galaxy, I don't see a clear path to the answer, and was hoping you could help. Either to confirm there is no tool or to suggest a dataflow. > > This is the thread so far, so you know where we are: > https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021146.html > https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021147.html > https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021148.html > https://lists.soe.ucsc.edu/pipermail/genome/2010-January/021149.html > > The short, the user has a list of novel SNPs and wants to know the change to the protein (perhaps also novel based off genomic). We have a web-mRna translation tool, but the user would then need to do the rest on his own: cut out the coding region, swap in the SNPs, translate via web tool, then analyze against a protein matrix for synonymous or non-syn changes. Protein only so far (although where they are taking it next - structural or functional implications, etc. we don't know - that is beyond the scope of the analysis we support, so far). > > Is there a Galaxy tool or workflow that you could suggest? If yes, should I forward the question on to the galaxy help list? Would that be the right place to send it? Or would you want to send me the info (I would credit you in the response unless you ask me not to - or the general galaxy help email if that is better)? If there isn't a tool, please let us know. > > Meanwhile, we are also checking around here for some development programs that *may* do this kind of thing. But obviously an existing Galaxy tool/workflow would be better. > > Thanks! And if I should be using someone else as a point person, please let me know and I'll spread the word over here. > > We appreciate your help! > jen > > Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

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eprimer3 missing?
by Erick Antezana 29 Jan '10

29 Jan '10

Hi, I have seen that many tools from EMBOSS have already an "XML tool file" (.../tools/emboss_5/*.xml). I couldn't find the one for eprimer3 (it seems it was there before? as it could be seen in ./.hg/store/fncache : data/tools/emboss/emboss_eprimer3.xml). I have looked for it in the bitbucket but I couldn't find it... Has it ever existed? or should I create myself an XML for such tool? cheers, Erick

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Maq output
by Michaela Lee 29 Jan '10

29 Jan '10

Does anyone know if Maq can produce alignment data in SAM format? Currently we can only generate outputs in fastq format. Is there a way Galaxy can convert a fastq file to a SAM file? I did not see it as an option but I thought I'd ask. Thanks! Michaela

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pysam egg
by Erick Antezana 28 Jan '10

28 Jan '10

Hi, I've just updated my Galaxy install. Everything works fine. I only had an issue while trying to use the pysam egg. The error message is the following: ImportError: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home/bio/erick/.python-eggs/pysam-0.1.1-py2.4-linux-x86_64.egg-tmp/pysam/csamtools.so) Unfortunately, we have in our system GLIBC 2.5 (glibc-2.5-42.el5_4.2). We have tried to bypass such requirement by compiling pysam and manually copying the csamtools.so file without success. Once I try to launch Galaxy (run.sh) it fetches the original egg (and so library)... The variable FETCH_EGGS was set to 0 but it is still fetching the latest versions...Are we missing something? Otherwise, would it be possible to have such egg for glib 2.5 ? thanks, Erick

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Re: [galaxy-user] GALAXY Question
by Guruprasad Ananda 27 Jan '10

27 Jan '10

Hi Mike, Do you mind sharing your history with me (guru(a)psu.edu) so that I can take a look at what might be going on? Thanks, Guru. > From: Michael Wilson <michael.d.wilson(a)gmail.com> > Date: January 26, 2010 12:43:30 PM EST > To: Anton Nekrutenko <anton(a)bx.psu.edu> > Subject: Re: [galaxy-user] GALAXY Question > > Dear Anton, > > I have a question regarding the 'Base Coverage' function. I have a 9 column interval file and when I perform 'Base coverage' it reports 0 bp of sequence despite there being many intervals. If I convert the same file to a bed file and then perform 'Base Coverage' I get the correct number of basepairs. There does not seem to be any problem with my interval files. I was wondering if this may be a bug. > > As I would like to use 'Base Coverage' in one of my workflows I tried to get around this problem by converting my interval files to bedfiles with 1:chrom 2:start 3:end (I do not indicate strand or name in these bedfiles). However when I use Filter and Sort: Select > ^chr21 , the new bedfile which is created with only lines starting with chr21 has for some reason had column 6 replaced with '+' and is labelled as 'strand' and column 8 is labeled with 'name'. I am not sure why the bedfile changes format after using the select command and if this is intentional or if you know a way around this happening. > > 1) can you use Base Coverage on interval files? > 2) is there a way to avoid changing the column designations in a bedfile when using Filter and Sort: select. > > > Thank you again for all your help and excellent resources. > > Best regards, > > Mike

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Re: [galaxy-user] [galaxy-bugs] workflow database
by Jeremy Goecks 25 Jan '10

25 Jan '10

Hi Jason, In the last couple weeks we've written the infrastructure that (a) enables users to publish workflows and (b) provides a way to browse, search, view, and use published workflows. (Histories and pages will have the same functionality as well.) This code is making it's way to our main webserver (it's being tested right now), and it should become available within the week. FYI, the links for published items will be: http://main.g2.bx.psu.edu/workflow/list_published http://main.g2.bx.psu.edu/history/list_published http://main.g2.bx.psu.edu/page/list_published Finally, a good place to pose these types of questions is galaxy-user, which I've CC'ed Best, J. On Jan 24, 2010, at 3:18 PM, Jason Miller wrote: > Hi I'm a user of galaxy and I was wondering if there is a database or website where users can submit workflows to be public? I know it's possible to make links or share with other users, but I thought it would be a good idea to have a database of workflows for everyone to see. > Thanks > Jason > > > > > > > > > > > > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs

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Re: [galaxy-user] alignment question
by Anton Nekrutenko 23 Jan '10

23 Jan '10

Michaela: Sorry for delay in replying. Looks like you need to do this: 1. Map reads with bowtie using "try hard" option. 2. Leave -m option at -1 3. Set -k ridiculously high (e.g., 1000) 4. Once mapped filter SAM with "SAM Tools->Filter SAM on bitwise flag" filter tool using option as in the attached image 5. Convert SAM format to intervals using "Covert SAM to interval" tool. 6. Subtract coordinates of regions from the previous step from coordinates of your exons using "Operate on Genome Intervals- >Subtract" tool. The result will contain unmapped regions. Let me know how it goes, and always cope to galaxy-user mailing list. Thanks, anton galaxy team On Jan 20, 2010, at 2:16 PM, Michaela Lee wrote: > Hi Anton, > > I am sorry to keep bothering you but could you clarify a bit more on > what I can do with mapped reads on Galaxy? Here is my situation: > We have attempted to sequence all the exons on the X chromosome for > some of our subjects through exon capture and high through-put > sequencing. We have all the Illumina reads on an external hard > drive and would like to know which regions of our reference sequence > were not "captured" or sequenced after mapping all the reads using > Maq or Bowtie. We are not interested in unmapped reads, just the > unmapped regions of the reference sequence. > > I have watched video #7 of Galaxy but I am confused as to which > "bitwise flag" I would use to have Galaxy generate an output file > with a list of regions of the reference sequence that were not > mapped. Ultimately, we would like to compare all the regions that > were not captured for all our subjects to see if those unsequenced > regions are random or not. > > I appreciate any help you can give me. Thank you! > > Michaela Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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Sharing Histories, Workflows, and Pages
by Jeremy Goecks 21 Jan '10

21 Jan '10

Hi all, Changeset 3253 stabilizes Galaxy's item sharing; items that can be shared are histories, workflows, and pages. There are now three types of sharing for items: (1) sharing via email with other users (unchanged); (2) making an item accessible via link (similar to 'enable import via link'); and (3) publishing an item. Sharing via email is unchanged; you can share item with individual users by specifying their email addresses. Making an item accessible via link generates a human-readable link that can be shared with other people; via this link, users can view or import an item. Publishing an item makes the item accessible via link and lists the item's link in Galaxy's public repository so that anyone via browse or search for it. Hence, in reference to a previous discussion about item sharing, it is now possible to generate a link for accessing an item but not publish the item's link. This changeset is available now in our development repository and will make its way to our dist repository and our main server in the next week. Comments, questions, and suggestions are welcome. Thanks, J.

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alignment question
by Michaela Lee 16 Jan '10

16 Jan '10

Hello, I was wondering if Galaxy can align Solexa reads to a reference sequence. If not, can I upload my alignment data from Maq onto Galaxy and somehow work with that data online? Also, can Galaxy tell me which parts of the reference sequence have no reads aligned to them? I am basically trying to figure out which parts were not sequenced and compare those sequences between different subjects. Thanks for your help. M

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