Re: [galaxy-dev] installing software for Galaxy
Hi Mattias, We use a combination of mi-deployment and Brad's cloudbiolinux script ( https://github.com/chapmanb/cloudbiolinux) to install tools (including the biolinux ones). It requires some manual effort but has worked for us. The approach you describe sounds pretty good for packaged tools, I would just suggest to maybe create a script to automate the process as you go about installing all of the tools. If you decide to create the script, please conside sharing it. Good luck, Enis On Mon, Sep 5, 2011 at 2:22 PM, Mattias de Hollander m.dehollan...@nioo.knaw.nl wrote: Hello Galaxy-developers and community, I would like to ask your advice on installing software. I used the cloudman scripts to install galaxy on a multi-core server. I use the fabric scripts from cloudman/mi-diployment to install some software but I am also looking at repositories like biolinux and the NBIC RPM repository. There has been a thread about that over here: http://gmod.827538.n3.nabble.com/RPM-repository-for-NGS-tools-in-Galaxy-tp2617820p2617820.html As James says in that thread I also prefer to install software in isolated directories to keep track of different version. Did someone use the biolinux repository to install software in a galaxy accepted path: $GALAXY_APPS/package/version/? How does the Galaxy Cloud team does that? (Enis?) I was thinking to use 'sudo apt-get --download-only' to first get the debs and then install them using 'dpkg --instdir' and then specifying the directory. Or is there a smarter way to do this? Any thoughts on this issue are appreciated. Thanks. -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] installing software for Galaxy
Hi Enis! Thanks for clarifying. One thing I can not find out is or Brad's scripts are installing the packages on system level or in a specific directory (like $GALAXY_APPS/package/version/). Suppose they are installed on the system level, how do you keep track of different versions? Thanks, Mattias On Mon, 2011-09-05 at 14:49 +0200, Enis Afgan wrote: Hi Mattias, We use a combination of mi-deployment and Brad's cloudbiolinux script (https://github.com/chapmanb/cloudbiolinux) to install tools (including the biolinux ones). It requires some manual effort but has worked for us. The approach you describe sounds pretty good for packaged tools, I would just suggest to maybe create a script to automate the process as you go about installing all of the tools. If you decide to create the script, please conside sharing it. Good luck, Enis On Mon, Sep 5, 2011 at 2:22 PM, Mattias de Hollander m.dehollan...@nioo.knaw.nl wrote: Hello Galaxy-developers and community, I would like to ask your advice on installing software. I used the cloudman scripts to install galaxy on a multi-core server. I use the fabric scripts from cloudman/mi-diployment to install some software but I am also looking at repositories like biolinux and the NBIC RPM repository. There has been a thread about that over here: http://gmod.827538.n3.nabble.com/RPM-repository-for-NGS-tools-in-Galaxy-tp2617820p2617820.html As James says in that thread I also prefer to install software in isolated directories to keep track of different version. Did someone use the biolinux repository to install software in a galaxy accepted path: $GALAXY_APPS/package/version/? How does the Galaxy Cloud team does that? (Enis?) I was thinking to use 'sudo apt-get --download-only' to first get the debs and then install them using 'dpkg --instdir' and then specifying the directory. Or is there a smarter way to do this? Any thoughts on this issue are appreciated. Thanks. -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Adding an OpenID provider to Galaxy
Hi, I have been trying to add a new OpenID provider to the Galaxy-hardcoded list of providers. I type in my credentials in the new provider's window, but I got the following error (I am giving here only the last five lines) Module openid.consumer.consumer:413 in complete Module openid.message:167 in fromPostArgs Module openid.message:200 in _fromOpenIDArgs Module openid.message:240 in setOpenIDNamespace InvalidOpenIDNamespace: Invalid OpenID Namespace u'http%3A%2F%2Fspecs.openid.net%2Fauth%2F2.0' Does anybody have an idea what in my server goes wrong with the OpenID Namspace and how I can fix it? It might be useful to say that my Galaxy database is located on a separate machine with an SSL connection form the Galaxy app server. Thank you in advance Nikolai -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] adding display application in local instance of galaxy
Hi All ,
i am working in galaxy tool . i want to add one visualization tools
in galaxy . i don't understand how the display applications works .
tag ox xml file is not clear for display application .
can u just explain the meaning of type=template tag , target_frame
tag , amp tag ,BASE URL , strip tag and viewable tag in this xml?
display id=genetrack_interval version=1.0.0 name=view in
link id=genetrack name=GeneTrack
url
target_frame=galaxy_mainhttp://genetrack.g2.bx.psu.edu/galaxy?filename=${encoded_filename.qp}amp;hashkey=${hash_key.qp}amp;input=${qp(str($genetrack_file.id))}amp;GALAXY_URL=${galaxy_url.qp}/url
param type=data name=bed_file viewable=False
format=bed6,genetrack/ !-- for now, we'll explicitly take care of
the multi-step conversion; walk genetrack datatype down as a
conversion of genetrack to genetrack doesn't exist and would likely be
pointless --
param type=data dataset=bed_file name=genetrack_file
format=genetrack viewable=False /
param type=template name=galaxy_url strip=True
${BASE_URL}/tool_runner?tool_id=predict2genetrack
/param
param type=template name=hash_key strip=True
#from galaxy.util.hash_util import hmac_new
${hmac_new( $APP.config.tool_secret, $genetrack_file.file_name )}
/param
param type=template name=encoded_filename strip=True
#import binascii
${binascii.hexlify( $genetrack_file.file_name )}
/param
/link
/display
Regards
shashi shekhar
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Re: [galaxy-dev] installing software for Galaxy
Mattias; Thanks for clarifying. One thing I can not find out is or Brad's scripts are installing the packages on system level or in a specific directory (like $GALAXY_APPS/package/version/). The script installs them at the system level, primarily using the package manager. There are some custom install scripts where packages do not exist, but primarily the goal is to reuse the work from ready to go packages. Suppose they are installed on the system level, how do you keep track of different versions? It's using the native package manager facilities for this. It doesn't allow custom injection of specific versions like Enis' setup or something like 'modules.' The main thing we're trying to avoid is having to hand maintain a ton of installation instructions, which is why we use build off the package maintainers' work. Brad ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Feedback appreciated for new unified tabular format: GTrack
Dear Galaxy-dev guys! Our research group have the last years been developing the Genomic HyperBrowser (http://hyperbrowser.uio.no), which is a system for statistical analysis of genomic data, built on top of Galaxy. The system currently includes 17 hypothesis tests and 53 descriptional statistics. In the process of developing the HyperBrowser, we have experienced several shortcomings of the usual tabular formats for genomic datasets: BED, WIG, GFF, BedGraph, etc. This has lead us to define (yet another) format for genomic data: the GTrack format (short for Genomic Track). The format will hopefully be published in an article, currently under review (together with an extension of the XML format BioXSD, which supports many of the same properties as the GTrack format). In the process of article review, we would be very interested in the feedback from you guys, in order for the format to be as good as possible. The basic issues handled are the following: 1. The first issue is the very existence of so many formats. We have, in the article, defined 15 different track formats and believe that these track formats are the main reason for the proliferation of tabular formats. The track formats are the usual Segments (as in BED) or Valued Segments (as in BedGraph), but also include other types as Points or Step Function. In addition, we introduce linked track types usable for analysis of three-dimensional data set. The GTrack format handles all 15 track types. 2. Simple to create. Allthough the GTrack format specification document is quite large, the format is still quite simple to handle. It is based on fixed columns (not attributes like GFF), but allows custom columns (unlike BED). If you allready have scripts creating output in a common tabular format, they should require little change to support GTrack. 3. Customizability. GTrack allows any number of custom columns to be added, in any order. Also, GTrack supports a scheme for creating GTrack subtypes. A GTrack subtype is a particular configuration of GTrack files explicitly created for specific uses/tools. All GTrack subtypes can still be handled by generic GTrack parsers. 4. Simple to parse. We have tried to make GTrack as simple as possible to parse. This includes the use of header lines for defining properties of a file. This eases parsing by telling the parses what is coming, plus it allows quick and dirty parsers to explicitly assert what they are able to handle (so as to abort with a clearly stated reason instead of failing silently). Also, the GTrack subtyping scheme allows parsers to limit their support to a subset of the GTrack specification, e.g. files with a fixed number and order of columns. 5. Advanced functionality. GTrack supports more advanced functionality such as networks of track elements and the option of defining the domain of a track (e.g. the genomic regions for which the track is defined). 6. Syntax, not semantics. As with BED or WIG, the GTrack format focuses on the structural elements of the data, e.g. how to represent data mathematically/informatically. We leave the specifics of interpretation to others (who can, for instance, use their definitons to create GTrack subtypes). We have also been in contact with the Galaxy team and have received positive signals regarding future support for GTrack in Galaxy. Note that tools for converting between GTrack and other formats, in addition to a tool to help create GTrack headers, will be available soon. We hope you find the format interesting and welcome all kinds of feedback/suggestions. As the paper is in a review process, we would appreciatee feedback within the next two weeks. Version 1.0b2 of the GTrack specification and an illustration of the 15 track types are available here: http://hyperbrowser.uio.no/hb/static/hyperbrowser/files/gtrack/GTrack_specification.txt http://hyperbrowser.uio.no/hb/static/hyperbrowser/files/gtrack/track_types.pdf For the HyperBrowser team, Sveinung Gundersen -- Sveinung Gundersen PhD Student, Bioinformatics, Dept. of Tumor Biology, Inst. for Cancer Research, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway E-mail: sveinung.gunder...@medisin.uio.no, Phone: +47 93 00 94 54 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
