November 2015 - galaxy-dev - lists.galaxyproject.org

developer details
by Mic 17 Nov '15

17 Nov '15

Hi, How do I find developer contact details, when I discover a bug in any wrapper? Thank you in advance. Mic

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Bug when reading in tab seperated files
by Christian Brenninkmeijer 17 Nov '15

17 Nov '15

Hi All, I noticed there is a bug when you read in tab separated files and leave them as type auto. These are then identified by https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/tabul… as "CSV" as the CSV type uses the python module "csv" which can read tab separated files. Fine so far EXCEPT that CSV's set_meta method does not read columns correctly if tab separated. def set_meta( self, dataset, **kwd ): ... reader = csv.reader(csvfile) #line 920 The default delimiter for ythins csv module is comma so a tab separated file file will have only 1 column. As a result especially in Planemo parameters of type type="data_column" will not work as the systems thinks there is only one column in the data. == The CSV data type needs to be fixed or to protect backward compatibility replaced. There are then several options for comma separated files. 1. Use python csv's sniff method to detect the delimiter in set_meta. This will result in a slow down and effect backward compatability. 2. Make CSV handle only comma separated files. Improve the def sniff( self, filename ): method (line 907) to make sure it is comma separated. There are various clean ways of doing this. 3. Create a new True_CSV type that sniffs only comma separated files but leave the old one for backward compatibility. For tab separated files 1. Above works here too 4 Then allow the default tabular to handle tab separated files. 5. Add a new type which extends True_CSV to sniff for tab separations and get_meta correctly with tabs. === I have code that works for True_CSV and the new TSV type if that is the best option. Christian University of Manchester 3b. Add one or more new types to handle tab separated files using pythons csv but informing python's csv reader of the new delimiter or dialect. regards Christian

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Tmhmm and signal P
by Olivier CLAUDE 16 Nov '15

16 Nov '15

Hello, I am installing this package from peterjc. I downloaded the tools from the CBS but i can’t run it in galaxy : TMHMM : galaxy gives the error : no output from tmhmm2 Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even launch it in command line) With v4.1 it can’t be reached by galaxy (I am thinking about something with the name 3.0 vs 4.1 but I can’t figure where I have to change …) Do anybody have an idea? Regards, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 – Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris

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Working with SLURM (same partition as cmd line)?
by Raymond Wan 15 Nov '15

15 Nov '15

Hi all, I was wondering if anyone has experience with setting up Galaxy with SLURM. I'm not sure if this is the same for other DRMAAs, but what I would like to do is use a server for both Galaxy and command-line job execution. Thus, I would like both to add jobs on to the *same* queue (i.e., partitions in SLURM). I guess this is technically possible, but are there any reasons that would make doing this a bad idea? I can't think of any and thought I'd ask to see if anyone knows. (I wished we could have a server dedicated to Galaxy and another dedicated to command-line usage, but we don't have such resources to do that.) I guess if I run "bwa" (for example) on the command-line, users would see "bwa" in the job list owned by me. Maybe if I run it through Galaxy, users might see the galaxy user being the owner. If that's the case, that is fine. But, other than this, is there something else that would make it a bad idea? For example, jobs run slower, SLURM behaving incorrectly, etc. Thank you! Ray

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Tool request: Integration von SecretomeP v1.0 in Galaxy
by Florian Sigloch 12 Nov '15

12 Nov '15

Dear Galaxy Developers, I would like to have this tool integrated into Galaxy. It is similar to SignalP, however, where SignalP predict conventional secretion / membrane integration, SecretomeP predicts unconventional secretion. More information is in the attached paper. A browser-version of SecretomeP v2.0 is available at http://www.cbs.dtu.dk/services/SecretomeP/ However, it is restricted to 100 uploaded sequences, so processing of large datasets is tedious. Therefore, integration into Galaxy would be great! A portable version of SecretomeP exists and is available here: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?secretomep It is only v1.0, but the difference between the versions is minimal (see also attached email of the developers). There is one caveat: SecretomeP can deal with sequences only up to 4,000 amino acids (I am not sure, if including or excluding the 4,000). It would be great to integrate a small preselection to sort out longer sequences into the Galaxy tool. Kind regards, Florian Sigloch P.S.: I am currently writing up my PhD thesis and I am short on time. Would it be possible to integrate SecretomeP in 2-4 weeks? Pleeeeease? P.P.S.: I have been in contact with Dr. Björn Grüning about this, but I do not want to bother him during his current trip to the US.

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IPython and Rstudio are missing
by Mic 12 Nov '15

12 Nov '15

Hello, Last week, I cloned Galaxy from Github. I uploaded a VCF file from my computer. I also installed the following additional software: *apt-key adv --keyserver keyserver.ubuntu.com <http://keyserver.ubuntu.com> --recv-keys E084DAB9* *echo 'deb http://cran.r-project.org/bin/linux/ubuntu <http://cran.r-project.org/bin/linux/ubuntu> trusty/' >> /etc/apt/sources.list* *apt-get -qq update && apt-get install --no-install-recommends -y libcurl4-openssl-dev libxml2-dev* *apt-get install apt-transport-https python-dev libc-dev pandoc pkg-config liblzma-dev libbz2-dev libpcre3-dev* *apt-get install libblas-dev liblapack-dev gfortran libzmq3-dev curl* *apt-get install libfreetype6-dev libpng-dev net-tools procps r-base libreadline-dev * *pip install distribute --upgrade* *pip install scipy sklearn-pandas bioblend matplotlib patsy pysam khmer ggplot mpld3 sympy rpy2* *pip install pyzmq ipython==2.4 jinja2 tornado pygments numpy biopython scikit-learn pandas* However, clicking the *visualize* icon no iPython and RStudio are visible. Galaxy is in my home folder installed */home/lorencm/galaxy.* What am I missing? Thank you in advance. Mic

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Galaxy Startup Failing
by Keith Suderman 11 Nov '15

11 Nov '15

Greetings, I am trying to upgrade our Galaxy instance to the latest stable code from master and now our instance won't start using my /etc/init.d/galaxy script. That is: > sudo service galaxy start no longer works. It says it does (i.e. prints "[OK]"), but Galaxy isn't running and nothing is written to the log. I am using the init.d script from simison [1], which is basically the same as the one posted to the Galaxy wiki [2], both of which are quite old. Galaxy does start with: > sudo su galaxy > ./run.sh --daemon so I have left Galaxy running in a screen session for now, but that is less than ideal. I suspect something to do with the .venv as `./run.sh --skip-venv` also fails and I don't recall Galaxy being that finicky about a venv being active. Does anyone know how I can get the /etc/init.d/galaxy script (i.e. start-stop-daemon) to activate the venv for paster.py? Cheers, Keith 1. http://simison.com/brian/GalaxyAdmin_notes.html 2. https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28… ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

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Remote Contribution Fest - Metagenomics Tools and Workflows 30th December + 1st November
by Björn Grüning 10 Nov '15

10 Nov '15

Hello all, We are planning a remote contribution fest for Galaxy tool developers to hack and data scientists to develop, document and create metagenomic Tools and Workflows. It will take place on 30th of November and 1st of December 2015! The remote nature of this should give people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Hopefully having a well defined topic will allow us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly. We have been collecting ideas to work on here - https://github.com/galaxyproject/tools-iuc/issues/299, but feel free to contribute your own ideas and enhancements to rock the metabolic world. If you are interested in participating in the codefest but not interested in actual tool development - we will assemble a list of small things everyone can contribute. So we explicitly invite everyone that is interested on metagenomics in Galaxy - Galaxy Scientists welcome! This is the second remote codefest we will organize and we encourage ideas or advice about how to improve this - let us know. Thanks, Galaxy IUC

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feature request
by Ryan G 09 Nov '15

09 Nov '15

I'd put this into Trello, but Trello is blocked from my place of business... I have a data library with over 200 files in it. Half of them are "clipped" and the other half are not. I'd like to be able to search and display a subset of files in the data library. This will make selecting the files I want to import into my history much easier.

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Set Galaxy as server
by Djurdjevic, Marija 09 Nov '15

09 Nov '15

Dir Sir/Madam, I am working in the Center for Medical Research and my new task is to establish Galaxy as server. Could you be so kind to give me some basic instruction regarding the Linux distribution which is the most suitable and stable for Galaxy? I already tried with Centos 7 and Virtual Box, but it wasn't successful. Is there any good tutorial to follow during setting up? Thank you in advance. Kind regards, Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

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