October 2013 - galaxy-dev - lists.galaxyproject.org

URL problem
by Jennifer Jackson 02 Oct '13

02 Oct '13

Alper, Did you problem get resolved already? Maybe on the galaxy-dev(a)bx.psu.edu mailing list? I am posting it there in case it is still open. Please reply to let us know your current status. Please drop galaxy-user(a)bx.psu.edu from the to/cc on reply and future posts to this thread. Thanks and sorry if this one got missed, Jen Galaxy team On 8/26/13 10:43 AM, Kucukural, Alper wrote: > Hi, > I have a problem in galaxy to get host/domain name in two different > pages. > First one is in the tool installation from toolshed, I got the error > below, > > ##### > > > Not Found > > The requested URL /admin_toolshed/prepare_for_install was not found on > this server. > > ##### > > The second one is in the saved histories. When I click the buttons of > the saved histories. I got the similar error like below. > ##### > > > Not Found > > The requested URL /history/list was not found on this server. > > ##### > > I haven't seen these any other pages yet. > > My installation is working on LDAP authentication with Proxy. So, I > could not find a place to set the domain or host name in these two > places that they can actually find the requested URLs. > > In the paster.log file. I don't get any error when I install a tool > or go to another history. It doesn't report any error. > > Thanks for your help, > > Alper Kucukural > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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Toolshed Collaboration Issues
by Lance Parsons 02 Oct '13

02 Oct '13

I'm having some difficulty collaborating on a tool development in the toolshed. It seems to happen on the production toolshed as well as the testtoolshed. When I try to grant another user the ability to update a repository (or when the other person tries to add me) we get the following error: URL: http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=f49c56ded… File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/framework/__init__.py', line 98 in decorator return func( self, trans, *args, **kwargs ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/webapps/tool_shed/controllers/repository.py', line 2124 in manage_repository user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) ) File '/var/opt/galaxy/g2cmnty/galaxy_testtoolshed/lib/galaxy/web/security/__init__.py', line 60 in decode_id return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) ) File '/usr/lib/python2.7/encodings/hex_codec.py', line 42 in hex_decode output = binascii.a2b_hex(input) TypeError: Non-hexadecimal digit found Can anyone else successfully grant a user update permission to a repository? I've submitted an issue on Trello (https://trello.com/c/XYkqW3Lr) -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Slice bam
by jean_jasinski＠agilent.com 02 Oct '13

02 Oct '13

It seems like Slice_bam should be pretty straight-forward to use, but when I run it and give it a bed file that contains the human chromosomes with their lengths like this: chr1 1 249250621 chr2 1 243199373 for all chromosomes 1-22, X, Y. I don't get the reads on chr1 and 2; instead, all I am left with are the reads on the nonstandard chromosomes (the unmapped scaffolds). Any idea what I am doing wrong? Jean Jasinski

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Galaxy STARTUP ERROR!
by Giovanni Pascarella 02 Oct '13

02 Oct '13

Hi! I am trying to launch Galaxy locally but I'm getting the following error: tkx417:galaxy pascarellagiovanni$ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/__init__.py", line 4, in <module> from framework import expose File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/web/framework/__init__.py", line 40, in <module> from babel.support import Translations File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/support.py", line 29, in <module> from babel.dates import format_date, format_datetime, format_time, LC_TIME File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py", line 34, in <module> LC_TIME = default_locale('LC_TIME') File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 642, in default_locale return '_'.join(filter(None, parse_locale(locale))) File "/Users/pascarellagiovanni/Desktop/galaxy/eggs/Babel-0.9.4-py2.7.egg/babel/core.py", line 763, in parse_locale raise ValueError('expected only letters, got %r' % lang) ValueError: expected only letters, got 'utf-8' Anybody knows what this is about? Thanks, Giovanni

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Re: [galaxy-dev] Dynamic data library
by Hans-Rudolf Hotz 02 Oct '13

02 Oct '13

On 10/01/2013 03:53 PM, Cole, Nathan (NIH/NCI) [C] wrote: > Thank you both for your responses. I will be looking into both of these. > > With regard to the from_file option to add the sample selection into the tool: I assume this means that the metadata and everything is loaded into galaxy at the time the tool is run. This depends on how you write your tool. Do you just wanna read the ie fastq file or do you also wanna read the meta data. Also, how is the meta data accessible? eg. is it stored in a txt file at the same location as the fastq file? > Does this create a copy of the loaded file or simply read it in place? Also are there any efficiency issues created using this method, outside of the tool run time increase due to the load of the data taking place in-tool? It should just read it in place Hans-Rudolf > > Thanks, > Nathan > > -----Original Message----- > From: Hans-Rudolf Hotz [mailto:hrh@fmi.ch] > Sent: Tuesday, October 01, 2013 4:07 AM > To: Cole, Nathan (NIH/NCI) [C] > Cc: Martin Čech; galaxy-dev(a)lists.bx.psu.edu > Subject: Re: [galaxy-dev] Dynamic data library > > Hi Nathan > > > Do you have many tools working with those samples or just a few? If you only have a limited, predefined set of tools you might wanna consider adding the sample selection into the tool. > > You can use the from_file, or from_data_table options to dynamically create sample selection list. You can even drill down a hierarchical list. Have a look at ~/tools/annotation_profiler/annotation_profiler.xml > which uses the file > ~/tool-data/annotation_profiler_options.xml > > All you need to do is keeping the file in sync with the directory structure of your samples directory > > > Regards, Hans-Rudolf > > > > > > > On 09/30/2013 09:48 PM, Martin Čech wrote: >> Hi Nathan, >> >> Dannon answered similar question few days ago: >> >> There's an import mechanism in libraries that'll allow you to simply >> link to the file on disk without copy/upload. I believe the >> "example_watch_folder.py" sample script (in the distribution) does >> just this via the API, if you want an example. >> >> >> This might be what you are looking for. >> >> Martin >> >> >> On Mon, Sep 30, 2013 at 2:43 PM, Cole, Nathan (NIH/NCI) [C] >> <nathan.cole(a)nih.gov <mailto:nathan.cole@nih.gov>> wrote: >> >> Hello, we’ve set up a local Galaxy instance in our genotyping and >> next-gen sequencing lab with local Apache LDAP (AD) integration, NFS >> mounts to a large NAS, and cluster integration coming. Do to the >> high volume of samples and staff that will be using the system, I >> want to set up data libraries (without copying to Galaxy). This is >> obviously no problem the first time, however I was wondering if >> there was a way to make a library, added from a system path, be >> dynamic so that it would stay synchronized with the underlying file >> structure?____ >> >> __ __ >> >> If a try dynamic library is not possible, is there a method for >> adding files to an existing library via that same system path that >> would not duplicate all of the original files in the data library?____ >> >> __ __ >> >> I did some scouring of the list and found some old unanswered >> questions and some things tangentially related topics, but I was >> unable to find a true answer or solution to my problem. Any >> information on how to do the tasks above or other solutions to >> provide the same functionality would be greatly appreciated.____ >> >> __ __ >> >> Thanks,____ >> >> Nathan____ >> >> __ __ >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >>

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how to generate .len file for custom genome? (trackster error)
by Ben Gift 02 Oct '13

02 Oct '13

Trackster complains to me when I try to load up my custom reference genome to compare some sample data to. "could not load chroms for this dbkey" I think it's because I'm using the newest g1k human ref genome v37, and I don't know if the hg19.len file works with it... I generated my own twobit file for it, but now I think I need the .len file... To be honest I'm kind of lost. Where does trackster even look for my genome, and how do I generate a .len file? (I read the visualizations page and the custom genome docs page)

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Test post, please ignore
by Guest, Simon 01 Oct '13

01 Oct '13

(Just testing that my Exchange Server admin guy has managed to disable the stupid legal disclaimers on my postings to this list.)

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configuring auth_ldap for galaxy
by Iry Witham 01 Oct '13

01 Oct '13

Hi Team, Has anyone had any experience with setting up auth_ldap for nginx? I am attempting to make this work, but nginx fails to start with the following message: Starting nginx nginx: [emerg] unknown directive "auth_ldap_url" in /usr/local/nginx/conf/nginx.conf:48 startproc: exit status of parent of /usr/local/nginx/sbin/nginx: 1 failed Any help would be appreciated. Thanks, Iry Witham The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Local Galaxy Install - Debug Report FROM address as Admin and not User?
by Adam Brenner 01 Oct '13

01 Oct '13

Howdy, On our local Galaxy install, everytime a user submits a bug report, it does email all the admins -- as defined in universe_wsgi.ini -- but the FROM address is not of the user, but rather the first email address from the admin list. Is this normal? May we have it changed so the FROM address is that of the user? Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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2 RNAseq files in queue to map w/Tophat in Main since last Thursday, please advise
by Theresa Stueve 01 Oct '13

01 Oct '13

Greetings, I have had two RNAseq files in queue to map with Top hat in Galaxy Main since last Thursday (History began Sept 19). Yesterday I got word that NGS was stalled, my jobs were mistakenly believed to be moving afterwards when they weren't- but are now under review again. This morning the 2 mapping jobs are still waiting to run. I have a data review meeting this thursday and hope you can advise me on contingency plans to get these 2 mapping jobs running. Can you tell me whether I should delete the jobs and re-run them as new? My concern is that they are still "believed to be moving" as was indicated by one of your galaxy stewards, but are actually still stalled in space. I have a data meeting Thursday (10/4) and hoped to be ready by starting this project Sept 19th. Can you tell me if you are aware of another public Galaxy server (other than Main) with 'Top Hat' for mapping RNAseq data? I joined Cistrome (Harvard) but they only have Cufflinks (for previously mapped RNAseq analysis) below is my history thank you very much for your help https://main.g2.bx.psu.edu/u/trstueve/h/rnaseqjegcsc3wkrun130924-1 <https://main.g2.bx.psu.edu/history/sharing#> Theresa Ryan Stueve 510-225-8894 (text better than voicemail for quick response)

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