galaxy-dev September 2009

galaxy-dev@lists.galaxyproject.org

15 participants
140 discussions

Re: [galaxy-dev] Managed releases?
by Chris Cole 08 Sep '09

08 Sep '09

Reposting to galaxy-dev list. Just realised this went off-list. Stewart Stevens wrote: > Hi Chris > > Yep, I feel the same way about dealing with our galaxy server in Otago. > Basically I just delay updating and then backup and bite the bullet > expecting to potentially run into problems. Of course the delay makes > these more likely. Ideally I guess I should update often and deal with > problems as they come, reporting these / fixes back to PSU. I just > don't have time to do this. Yup. My sentiments exactly. Except here we have two parallel installs; one that can be broken and one that should be 'stable'. > I should be spending my time researching > gout genetics! (I used to be a professional software engineer.) I'm not a software engineer, I want to use the best tools to be able to do my research. Occassional debugging and fixing things is fine. > You're right that just a change log and some release markers would be > helpful. > > Cheers, > > Stewart > > > > > On 8/09/2009, at 9:57 AM, Chris Cole wrote: > >> Hi Stewart, >> >> I agree with you that PSU are doing a fantastic job with galaxy at the >> moment and it's great to be able to get hold of the latest and >> greatest commits to the repo. This is part and parcel of academia; >> exciting new tools with some rough edges. >> >> However, we don't update our galaxy server on a regular basis as we're >> happy to work with what we have, but now and again I would like to >> know what updates have been made to the development tree and how >> significant they are /before/ I do an update. i.e. has recent activity >> been mainly bugfixes or has some major new functionality been added? >> At the very least a chagelog would be good or even some version numbers. >> >> I'm not asking for a highly managed and robust testing regime on all >> common platforms with fancy installers etc. Just an idea of what's >> changed between my current install and the latest on the trunk, but at >> a higher level than file diffs. >> Cheers, >> >> Chris >> >> >> Stewart Stevens wrote: >>> Hi, >>> Managed, documented, quality controlled releases? From the >>> perspective of someone outside PSU installing a local galaxy service >>> this would clearly be highly beneficial. >>> One point is that the research environment in which bioinformatics >>> software is developed often leads to a "serve it while its hot" >>> attitude, obviously the commercial world still wants hot releases >>> but pretty much everyone does some kind of release management - >>> inadvertently serving up rubbish would cause chaos in the supply >>> chain and damage reputations. >>> Academia isn't entirely different. I don't know what process the >>> guys at PSU go through when they update the servers running the >>> public release of galaxy but I'm sure they do have some process! So >>> could this be transformed into some kind of release management? >>> Possibly, but PSU has one particular environment and so any >>> rigourous release testing would need plenty of additional work. >>> Also when something does go wrong they are immediately able to make >>> necessary fixes - effectively making point releases. At the moment >>> we get to check out code and that does make it clear that it is >>> development stuff and the responsibility for testing lies with >>> whoever is installing it. Another advantage is that this engages the >>> community with the development effort. >>> A suggestion which could be good is to undertake marked releases as a >>> community. Just tag the repository at opportune intervals. Those >>> who want can work from that tag which can branch to a mature release >>> as bug reports are dealt with. This would still take resource to >>> manage centrally at PSU. I guess it is a sign of the product >>> maturing that people want managed releases. (Cool product btw!) I'm >>> sure we're all glad to have a great development branch rather than >>> some crappy managed releases. On the back of this, hopefully PSU >>> will be successful in attracting funding to continue development and >>> also package releases nicely. >>> Cheers, >>> Stewart >>> On 8/09/2009, at 9:12 AM, Chris Cole wrote: >>>> Anyone have any thoughts on this? >>>> >>>> Chris Cole wrote: >>>>> Hi, >>>>> >>>>> I have a local install of Galaxy and would like to keep up-to-date >>>>> with >>>>> the latest updates, but I'm not sure what functionality has changed >>>>> nor >>>>> how significant the changes are. The mercurial updates on this list >>>>> are >>>>> too detailed. I just want to know what the benefit of an update would >>>>> be, not which files have changed. >>>>> >>>>> Would it be possible to start having more managed releases with a >>>>> changelog between each release? That way it will be much clearer what >>>>> the functional benefits of updating to a newer release would be. >>>>> Cheers, >>>>> >>>>> Chris >>>>> >>>> >>>> _______________________________________________ >>>> galaxy-dev mailing list >>>> galaxy-dev(a)bx.psu.edu >>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev >> >

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Re: [galaxy-dev] How to use https protocol
by Aminah Keliet 04 Sep '09

04 Sep '09

Hi Nate, Biomart is running in https address, and i installed Galaxy in https address too. And, i want to include this Biomart on the data sources of Galaxy. But, the data from Biomart don't exported in Galaxy, because he want to connect in http (not https) to retrieve the results. Thanks for help, Aminah, -- Aminah Olivia KELIET Ingenieur d'études en Bio-informatique Unité de recherche en Génomique-Info INRA Centre de Versailles Route de Saint Cyr 78026 Versailles Cedex email: Aminah-Olivia.keliet(a)versailles.inra.fr url:http://urgi.versailles.inra.fr tel: 01.30.83.37.74

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EggNotFetchable: DRMAA_python
by Andreas Kuntzagk 04 Sep '09

04 Sep '09

Hi, I try to run a local galaxy installation with a sge job runner. But whenever I start run.sh I get an Traceback (most recent call last): File "/data/bioinformatics/galaxy/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/bioinformatics/galaxy/lib/galaxy/app.py", line 64, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 33, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/data/bioinformatics/galaxy/lib/galaxy/jobs/__init__.py", line 636, in __init__ import runners.sge File "/data/bioinformatics/galaxy/lib/galaxy/jobs/runners/sge.py", line 10, in <module> pkg_resources.require( "DRMAA_python" ) File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 558, in require if not egg.fetch(): File "/data/bioinformatics/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch raise EggNotFetchable( self.name ) EggNotFetchable: DRMAA_python some nodes: drmaa_python is installed and can be used by the galaxy user (if SGE_ROOT and LD_LIBRARY_PATH are set) I first used python2.6 and fell back to 2.5 but the problems stays the same. Any idea how to proceed? regards, Andreas

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Load Balancing
by Kimberly Begley 04 Sep '09

04 Sep '09

Hello, The load balancing page is showing up blank at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/LoadBalancing for me. Can you direct me to the correct URL for this info? Cheers, Kimberly

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How to use https protocol
by Aminah Keliet 03 Sep '09

03 Sep '09

Hi, I want to add Biomart (on protocol https) in the data source, but the "get data" don't retrieve the results from Biomart. In fact, Galaxy want to connect on http protocol (not https), to export the results. I obtain same results for all data source used in Galaxy (https protocol). It's normal? Please help me. Thanks, Aminah, -- Aminah Olivia KELIET Ingenieur d'études en Bio-informatique Unité de recherche en Génomique-Info INRA Centre de Versailles Route de Saint Cyr 78026 Versailles Cedex email: Aminah-Olivia.keliet(a)versailles.inra.fr url:http://urgi.versailles.inra.fr tel: 01.30.83.37.74

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Re: [galaxy-dev] [galaxy-user] headers in tabular datatypes
by James Taylor 02 Sep '09

02 Sep '09

Definitely possible (but as Greg said, not trivial). MetaDataElements define a schema for the allowed metadata on a given datatype. You'll always need that, in your case, you will define a new metadata element containing a list of column names. Then you'll want to override set_meta to try to detect the column names. (init_meta initializes with defaults, set_meta tries to detect from the data). Finally, you'll want to modify ColumnListParameter to use the names if they are defined. (As long as this is backward compatible, you could just add it to the Tabular datatype, and I'm pretty sure we'd be happy to integrate it, I've wanted this feature for a while. It just needs to be conservative about detecting headers to not break things that work now. For example, many UCSC formats include comment lines before the header, very difficult to detect properly). (Moving to galaxy-dev) On Sep 1, 2009, at 10:32 AM, James Casbon wrote: > Thanks, Greg. So you do think it is possible? I have tried to > understand the datatype by looking at: > http://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes > and reading the code. I am now very confused - when should you use > init_meta and set_meta, or a MetaDataElement ? > > It looks like MetaDataElements are class definitions, so to what > extent can you change metadata on an instance?

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Disabling viewing of very large files
by Chris Cole 02 Sep '09

02 Sep '09

Hi, We've come across a problem in our local Galaxy install with users trying to view extremely large files. This makes Galaxy slow to a crawl and has actually brought the server down due to out-of-memory errors. In order to avoid this is there a way to disable the view button for files of a certain type or above a certain size? Thanks for any help, Chris

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[hg] galaxy 2655: Updating .hgignore
by Greg Von Kuster 01 Sep '09

01 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9a4ce5d39cbb changeset: 2655:9a4ce5d39cbb user: James Taylor <james(a)jamestaylor.org> date: Sun Aug 23 12:35:00 2009 -0400 description: Updating .hgignore 1 file(s) affected in this change: .hgignore diffs (14 lines): diff -r 4dc854bf2529 -r 9a4ce5d39cbb .hgignore --- a/.hgignore Fri Aug 28 21:08:07 2009 -0400 +++ b/.hgignore Sun Aug 23 12:35:00 2009 -0400 @@ -20,3 +20,10 @@ reports_wsgi.ini datatypes_conf.xml tool_conf.xml +tool-data/*.loc + +# Test output +run_functional_tests.html + +# Project files +*.kpf

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[hg] galaxy 2656: Commenting out tagging fields, queries do not ...
by Greg Von Kuster 01 Sep '09

01 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d7a780065c91 changeset: 2656:d7a780065c91 user: James Taylor <james(a)jamestaylor.org> date: Sat Aug 29 12:08:35 2009 -0400 description: Commenting out tagging fields, queries do not seem to work on test 2 file(s) affected in this change: templates/dataset/edit_attributes.mako templates/root/history.mako diffs (55 lines): diff -r 9a4ce5d39cbb -r d7a780065c91 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Sun Aug 23 12:35:00 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Sat Aug 29 12:08:35 2009 -0400 @@ -4,7 +4,7 @@ <%def name="title()">${_('Edit Dataset Attributes')}</%def> <%def name="stylesheets()"> - ${h.css( "base", "history", "autocomplete_tagging" )} + ${h.css( "base", "autocomplete_tagging" )} </%def> <% user, user_roles = trans.get_user_and_roles() %> @@ -84,17 +84,17 @@ </div> <div style="clear: both"></div> </div> - %if trans.get_user() is not None: - <div class="form-row"> - <label> - Tags: - </label> - <div id="dataset-tag-area" - style="float: left; margin-left: 1px; width: 295px; margin-right: 10px; border-style: inset; border-color: #ddd; border-width: 1px"> - </div> - <div style="clear: both"></div> - </div> - %endif + ## %if trans.get_user() is not None: + ## <div class="form-row"> + ## <label> + ## Tags: + ## </label> + ## <div id="dataset-tag-area" + ## style="float: left; margin-left: 1px; width: 295px; margin-right: 10px; border-style: inset; border-color: #ddd; border-width: 1px"> + ## </div> + ## <div style="clear: both"></div> + ## </div> + ## %endif %for name, spec in data.metadata.spec.items(): %if spec.visible: <div class="form-row"> diff -r 9a4ce5d39cbb -r d7a780065c91 templates/root/history.mako --- a/templates/root/history.mako Sun Aug 23 12:35:00 2009 -0400 +++ b/templates/root/history.mako Sat Aug 29 12:08:35 2009 -0400 @@ -377,8 +377,8 @@ <p></p> %endif -<div id="history-tag-area" style="margin-bottom: 1em"> -</div> +## <div id="history-tag-area" style="margin-bottom: 1em"> +## </div> <%namespace file="history_common.mako" import="render_dataset" />

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requirements for a local production Galaxy server
by Kimberly Begley 01 Sep '09

01 Sep '09

Hello, Just want to confirm the requirements for a local production Galaxy server installation. >From what I gather they are: Python 2.4 or 2.5 Subversion or Mercurial Suggested optionally: MySQL Apache proxy server configs Sun Grid Engine Cluster configs and to be fully functional: perl EMBOSS, gnuplot, etc from the dependency list at http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies Please let me know if I'm missing anything. Cheers, Kimberly

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galaxy-dev September 2009