February 2010 - galaxy-user - lists.galaxyproject.org

setting environment for sge scripts
by Andreas Kuntzagk 15 Apr '10

15 Apr '10

Hi, I followed the advice for multiple installed python versions to set ~galaxy/galaxy-python/python and set the environment for the galaxy user to have that in the PATH Problem is, when a job is started on GridEngine, it does not use the "-V" flag to inherit the environment. So it runs with a different python version and more important it does not set LD_LIBRARY_PATH and fails for some tools which need some special lib. (libRblas in this case) Where can I fix that? regards, Andreas

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Small RNA gene, tRNA genes
by Kluger, Yuval 18 Mar '10

18 Mar '10

Hi, I would appreciate any suggestion how one can use Galaxy to obtain coordinates of human and mouse of all known tRNAs. Similarly how one can do that for other types such as miRNAs and other small RNAs . Thanks, Yuval ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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pre-loading data on server
by Brent Pedersen 25 Feb '10

25 Feb '10

hi, i have an instance of galaxy running on my own server. i'd like to have it preloaded with data and have that available to the users. say: thaliana_v9.gff and thaliana_v9.fasta . how do i do that? i've edited tool-data/faseq.loc and added: thaliana_v9 /opt/src/galaxy-server/localdata/fastas/ what else (or other) should i do? thanks, -brent

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Text editor
by Jelle Scholtalbers 25 Feb '10

25 Feb '10

Hi, is there a possibility to have a very basic text editor within Galaxy (or is there already one and I didn't find it)? I find myself saving files to my pc and uploading them again, or use some regular expression to edit my files, just to fix some small part that needs to be edited before it can go into a tool. Enabling a text editor for files not larger as they are provided by the 'display data' would be very helpful. Cheers, Jelle

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zip vs. gzip
by Pieter Neerincx 10 Feb '10

10 Feb '10

Hi, Can someone help me understand the automagic (un)zipping in Galaxy? In my universe_wsgi.ini there an option to enable gzip compression like this: # ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer ) # but you may also turn on Paste's built-in gzip compressor by uncommenting the following lines # and also the 'filter-with = gzip' line under [app:main]. This will reduce network traffic # and should speed up the interface, especially the visualization module. # [filter:gzip] use = egg:Paste#gzip ... filter-with = gzip 1. I cannot find instructions on how to enable gzip compression in Apache at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, but I have enabled "Paste's built-in gzip compressor" and that does not generate errors, so I guess it works. 2. This is not the part that is responsible for automatically detecting *.gz files and unzipping them, or is it? Enabling or disabling the code above does not affect automagic unzipping of uploaded *.gz, which works for me with or without the code above. 2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip.... Cheers, Pi

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Novice questions
by Mariette 08 Feb '10

08 Feb '10

Hi, I'm currently using ergatis as workflow manager, and I'm looking at the differences between ergatis and galaxy. In order maybe to migrate to galaxy. One really important feature to me is the ability of ergatis to iterate against file liste. I haven't seen anything like this in galaxy, am I mistaking ? Other point there is a way to make galaxy using local files instead of importing all files on the server ? And finaly I was wondering if there is a way to configure galaxy, so the outputs are stored to the ldap-user home directory ? thanks for your reply, Jerome

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Re: [galaxy-user] taxBuilder executable
by Anton Nekrutenko 08 Feb '10

08 Feb '10

Edward: The binaries are here: http://dist.g2.bx.psu.edu/ Let us know if you have trouble. Thanks, anton galaxy team On Feb 5, 2010, at 10:31 PM, Edward Kirton wrote: > oops, i should have specified that this is on my local install > > > On Feb 5, 2010, at 6:03 PM, anton(a)bx.psu.edu wrote: > >> Ed: >> >> Do you see this on your local install or on the main site? >> >> anton >> galaxy team >> >> >> >>> 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! >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> >> > Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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taxBuilder executable
by Edward Kirton 05 Feb '10

05 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 01 Feb '10

01 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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