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No Menu after submitting workflow
by Dave Walton 19 Apr '11

19 Apr '11

I'm getting inconsistent behavior when I run a workflow. I have one workflow,that when I run it, the green box indicating my workflow has been submitted shows up in the middle panel with Tools to the left, histories to the right, and menu above. For another workflow, I submit it successfully, but the green box ends up on a page with nothing but the green box. No tools, no history, no menus. Both of these are being done using the same browser session (running firefox on a mac). Thanks, Dave

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DRMAA_python installation problem
by Johannes Eichner 19 Apr '11

19 Apr '11

Dear Galaxy Team, I just updated my local instance of galaxy, and now I have a problem with the "DRMAA_python" egg, which makes it impossible to run jobs on our SGE cluster. I get the following error message after executing "run.sh": ____________________ Traceback (most recent call last): File "/rahome/webservices/galaxy_test/lib/galaxy/jobs/__init__.py", line 1028, in _load_plugin module = __import__( module_name ) File "/rahome/webservices/galaxy_test/lib/galaxy/jobs/runners/sge.py", line 28, in <module> raise Exception( egg_message % str( e ) ) Exception: The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's "scramble" system should make this installation simple, please follow the instructions found at: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster Additional errors may follow: ['DRMAA_python'] ____________________ I read the instructions and set the corresponding environment variable to tell galaxy about the location of the DRMAA library using the command: export DRMAA_LIBRARY_PATH=/opt/sge-6.1/lib/lx24-x86/libdrmaa.so.1.0 When I started galaxy again, the same error message (see above) occurred. I also tried to scramble the DRMAA_python egg, which resulted in the following error message: ____________________ fetch_one(): Using existing source, remove to download again: /rahome/webservices/galaxy_test/scripts/scramble/archives/DRMAA_python-0.2.tar.gz unpack_source(): Removing old build directory at: /rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python unpack_source(): Unpacked to: /rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python copy_build_script(): Using build script /rahome/webservices/galaxy_test/scripts/scramble/scripts/DRMAA_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /rahome/webservices/galaxy_test/scripts/scramble/build/py2.6-linux-i686-ucs4/DRMAA_python: /usr/bin/python26 scramble.py main(): Patching setup.py running bdist_egg running egg_info creating DRMAA_python.egg-info writing DRMAA_python.egg-info/PKG-INFO writing top-level names to DRMAA_python.egg-info/top_level.txt writing dependency_links to DRMAA_python.egg-info/dependency_links.txt writing manifest file 'DRMAA_python.egg-info/SOURCES.txt' reading manifest file 'DRMAA_python.egg-info/SOURCES.txt' writing manifest file 'DRMAA_python.egg-info/SOURCES.txt' installing library code to build/bdist.linux-i686/egg running install_lib running build_py creating build creating build/lib.linux-i686-2.6 copying DRMAA.py -> build/lib.linux-i686-2.6 copying cDRMAA.py -> build/lib.linux-i686-2.6 running build_ext building '_cDRMAA' extension creating build/temp.linux-i686-2.6 gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind\ -tables -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/sge-6.1/include -I/usr/include/python2.6 -c cDRMAA_wrap.c -o build/temp.linux-i686-2.6/cDRMAA_wrap.o -Wno-unused cDRMAA_wrap.c:13:20: error: Python.h: No such file or directory cDRMAA_wrap.c:358: error: expected specifier-qualifier-list before ‘PyObject’ cDRMAA_wrap.c:364: error: expected specifier-qualifier-list before ‘PyObject_HEAD’ ... error: command 'gcc' failed with exit status 1 Traceback (most recent call last): File "scripts/scramble.py", line 44, in <module> egg.scramble() File "/rahome/webservices/galaxy_test/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/rahome/webservices/galaxy_test/lib/galaxy/eggs/scramble.py", line 206, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for DRMAA_python 0.2 ____________________ I would very much appreciate your help in fixing this problem. Kind regards, Johannes -- Dipl.-Inf. (Bioinf.) Johannes Eichner Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 / 29 70436 Fax: (+49/0) 7071 / 29 5091

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Execution of workflows using API
by Takafumi Yamaguchi 19 Apr '11

19 Apr '11

Hello, I have a question regarding execution of workflows using API (workflow_execute.py). I am writing a script to automate file uploading and workflow execution using API. I was able to upload files and the response gave me ids for each file with 32 characters although the README example returned 16 characters. (I used library_upload_from_import_dir.py) Then I tried to execute a workflow using workflow_execute.py but it does not seem that the script accepts the ids. Is there any ways to resolve this issue? Thank you, Taka

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Setting min/max limit on <repeat> tag in tool XML file
by Peter Cock 19 Apr '11

19 Apr '11

Hi all, I'm working on a tool where the <repeat> tag looks like an elegant solution - however I want to limit the number of repeats to be 1, 2 or 3. i.e. I want to set min="1" and max="3" attributes for the <repeat>, based on analogy to the <param> tag. Is this possible, but not documented here? https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax In terms of the GUI, I'd like the page to preload with as many entries as the min setting (zero by default), and disable the add button once the max setting is reach (default no limit). (Alternatively you could validate the max/min when the form is submitted by clicking the execute button, but that seems less user friendly.) If this isn't already possible, would it be generally useful to add this? Thanks, Peter

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Re: [galaxy-dev] FTP upload of data
by Dannon Baker 19 Apr '11

19 Apr '11

Ok, great. Please do remember to reply-all and include the list in the future. Among other things, it helps us immensely in keeping track of what has and has not been answered. -Dannon On Apr 19, 2011, at 9:43 AM, vasu punj wrote: > I figured out and find files. Thanks. > > > --- On Tue, 4/19/11, vasu punj <punjv(a)yahoo.com> wrote: > > From: vasu punj <punjv(a)yahoo.com> > Subject: Re: [galaxy-dev] FTP upload of data > To: "Dannon Baker" <dannonbaker(a)me.com> > Date: Tuesday, April 19, 2011, 8:37 AM > > Dannon, > > I used winSCP to upload the files but dont see in Galaxy in history of uploaded files or even with URL? > > Any suggestion please. > > Thanks > > --- On Mon, 4/18/11, Dannon Baker <dannonbaker(a)me.com> wrote: > > From: Dannon Baker <dannonbaker(a)me.com> > Subject: Re: [galaxy-dev] FTP upload of data > To: "vasu punj" <punjv(a)yahoo.com> > Cc: galaxy-dev(a)bx.psu.edu > Date: Monday, April 18, 2011, 2:40 PM > > Vasu, > > No, a paid service is not at all required. jjw14's solution in that thread predates native FTP transfer to galaxy, and that sort of intermediate paid host is not necessary. > > Find detailed instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP > > -Dannon > > > On Apr 18, 2011, at 3:32 PM, vasu punj wrote: > > > Hi All, > > > > I was wondering if there are instructions for uploading data files (large) to Galaxy via FTP and if this is a paid service as per link : http://seqanswers.com/forums/showthread.php?t=5328 > > > > > > Thnaks. > > > > Vasu > > ___________________________________________________________ > > 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/ >

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Re: [galaxy-dev] FTP upload of data
by Dannon Baker 19 Apr '11

19 Apr '11

To be clear, you were able to connect to the galaxy server using WinSCP in plain FTP mode, and had no errors uploading the files? -Dannon On Apr 19, 2011, at 9:37 AM, vasu punj wrote: > Dannon, > > I used winSCP to upload the files but dont see in Galaxy in history of uploaded files or even with URL? > > Any suggestion please. > > Thanks

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Galaxy Tool Shed:- Uploading tool packages fails with Server Error message
by Vipin TS 19 Apr '11

19 Apr '11

Dear Galaxy team, I would like to upload a set of converter programs available for Generic Feature Format (GFF). When I tried to upload to Galaxy tool shed using my user name vipin.ts(a)tuebingen.mpg.de, it gives me Server error message. I am using a *.bz2 file for uploading. It will be great if you can have a look on this issue. thanks in advance, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824

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Update problem
by Olen Vance Sluder Jr 19 Apr '11

19 Apr '11

I was trying to update my existing Galaxy installation to the latest release (50e249442c5a) and encounter the following when I start it up: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 11, in ? from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/home/galaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in ? from galaxy.web.base.controller import UsesHistory File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in ? from galaxy.visualization.tracks.data_providers import get_data_provider File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 13, in ? from galaxy.datatypes.util.gff_util import * File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/util/gff_util.py", line 152 finally: ^ SyntaxError: invalid syntax I have attached the full script of what I did. I'm not too familiar with Mercurial and couldn't find any guidance in the wiki or mailing list on exactly what choices to make when Mercurial encountered conflicts, so I accepted the "delete" or "other" options when these occurred. Any help would be appreciated. Thanks, Olen

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FTP upload of data
by vasu punj 18 Apr '11

18 Apr '11

Hi All, I was wondering if there are instructions for uploading data files (large) to Galaxy via FTP and if this is a paid service as per link : http://seqanswers.com/forums/showthread.php?t=5328 Thnaks. Vasu

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Email notification and Workflow sharing for all users
by Paul, Rohit (NIH/NCI) [C] 18 Apr '11

18 Apr '11

I apologize for reposting this, but I really need some advice on how to meet this requirement: >From what I understand about Galaxy so far, in order to have a user notified that their job has completed, a workflow has to be created in which email notification is chosen as a "Step Action". For the project that I'm currently working on, I need to have a link to one particular workflow appear in the Tools left-hand side panel/frame for every user that logs in to Galaxy. They shouldn't have to import the specific workflow — it should automatically be listed. I know that I can create links in the Tools panel, but it seems that in order to access a workflow (via direct URL such as: '/workflow/run?id=12345') the logged in user has to either be the creator of the workflow or the creator has to have explicitly "shared" the workflow with the user. Is there a way to grant "share" permission on a workflow to all logged-in users, so that I can list it as a Tool link and it shows up for all users, current and those who may register in the future? Or is there some other approach I can/should take to enable job completion notification for all logged-in users? -Rohit

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