galaxy-dev April 2011

galaxy-dev@lists.galaxyproject.org

78 participants
133 discussions

Plotting tools - best output format? PDF, PNG, ...
by Peter Cock 20 Apr '11

20 Apr '11

Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the "eye" button acts like a download link. Is this a bug? If I switch to making a PNG file, then clicking on the "eye" button shows the image directly in the center panel (nice), but PNG is not a great format for detailed figures or printing. Looking over the tools which come with Galaxy under tools/plotting/*.xml all use PDF or PNG. How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Peter

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Re: [galaxy-dev] Execution of workflows using API
by Dannon Baker 20 Apr '11

20 Apr '11

Taka, Great, I'm glad the workflow api is now working for you. I'm not sure what you mean with regards to work I'm doing for decrypting hda to actual id, but I will say that a History/Dataset API is something many people have asked about and I imagine that it will get done sooner rather than later, though I can't specify an exact timeframe. -Dannon On Apr 20, 2011, at 11:29 AM, t.yamaguchi(a)utoronto.ca wrote: > Hello Dannon, > > Thanks for the quick response. > I emailed you as it seems to take some time to get authorization to reply to posts. > > I went though example_watch_folder.py and found the answer to resolve my problem. I thought the ids that returned from library_upload_from_import_dir.py were ldda but it was ld. Thanks. > > I have another question. > I would like to access output files from each history using my script. > I saw your previous posts and you're working on API to decrypt hda to its actual id. > Are you planning to release the script in the near future? > > Thank you, > > Taka > > -------------------------------------------------------------------- > > Taka, > > Would you mind sharing the exact command you used to call > workflow_execute.py? > > It does sound like you're doing something very similar to what > scripts/api/example_watch_folder.py does. That script also uploads from > the file system to a data library and subsequently executes a workflow > on the uploaded files. If you haven't already taken a look there, it > could perhaps serve as another example for you. > > -Dannon > > On 04/19/2011 10:51 AM, Takafumi Yamaguchi wrote: > >> 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 >> >> ___________________________________________________________ >> 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/ > « [hide part of quote]

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BLAST+ HTML output broken
by Peter Cock 20 Apr '11

20 Apr '11

Hi Kanwei, I noticed that the BLAST+ output options for HTML are not working, a side effect of my recent refactoring. Could you transplant/merge this fix and test please: https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf https://bitbucket.org/peterjc/galaxy-central/changeset/c60551f7d13c These are the only commits on this new branch from the default: https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_04_19 Thanks, Peter

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No Menu after submitting workflow
by Dave Walton 20 Apr '11

20 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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galaxy-dev April 2011