Re: [galaxy-dev] macs in galaxy
Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce ko...@gis.a-star.edu.sgwrote: In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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/ ___ 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 local instance hiccup
Hi Stephen, What platform are you running on? Thanks, K On Wed, Aug 24, 2011 at 3:53 AM, Stephen Doyle s.do...@latrobe.edu.auwrote: Hello, I am in the process of installing a local instance, and I can't seem to be able to build the bx_python egg, even with scramble.py. Any ideas to get around this? Cheers, Steve - Dr Stephen R. Doyle Postdoctoral Researcher Genetics Department | La Trobe University | Bundoora 3086 Australia T: +61 3 9479 3087 | F: +61 3 9479 2480 | E: s.do...@latrobe.edu.au | W: http://www.latrobe.edu.au/genetics/staff/stephen_doyle.htm *La Trobe University - ranked top in Victoria for student satisfaction (Sweeney Uni Student Report, 2009) * CRICOS Provider 00115M J Please kindly consider your environment before printing this e-mail Warning to recipients: This email and any attachments are confidential and subject to copyright. If you are not the intended recipient any use, disclosure or copying is unauthorised. If you have received this email in error please advise us immediately by reply email and delete all copies. It is your responsibility to examine this email and any attachments for viruses. Any personal information in this email must be handled in accordance with the Information Privacy Act 2000 (Vic). ___ 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/ ___ 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] Error when using build_profile_indexes.py on hg19
Hi Sarah, Sorry for the late reply. The error is related to a bug we're currently looking into. If you run it again, does it have this error consistently or does it only happen once in a while? Thanks, K On Thu, Jul 7, 2011 at 12:11 PM, Sarah Diehl di...@immunbio.mpg.de wrote: Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_**profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/** wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal (/galaxy/galaxy_data/ucsc_**data/hg19/**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (**wgEncodeOpenChromFaireGlioblaB**aseOverlapSignal) directory (profiled_annotations/hg19/**wgEncodeOpenChromFaireGlioblaB** aseOverlapSignal). Created table dir (profiled_annotations/hg19/** wgEncodeCshlShortRnaSeqK562Chr**omatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File /galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_** profiler/build_profile_**indexes.py, line 338, in module if __name__ == __main__: __main__() File /galaxy/galaxy_backup/galaxy-**dist/scripts/tools/annotation_** profiler/build_profile_**indexes.py, line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File bitset.pyx, line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File bitset.pyx, line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah __**_ 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/ ___ 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] Launching a JAVA or external app
Hi Alex, Sorry for the late reply. Can you elaborate more on your needs? Does the Java app require filenames/params that can't be passed through the command line? Thanks, K On Mon, Jun 27, 2011 at 9:57 AM, Bossers, Alex alex.boss...@wur.nl wrote: Hello all, would it be possible to launch for instance a JAVA app with preloaded parameters and files from galaxy that needs interaction/display? For instance a gui based annotation editor? It necessarily doesn't have to support saving of files back to galaxy. Sort of end stage. Any help or pointers appreciated. thanks Alex ___ 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/ ___ 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] Sam2interval.py bug
Hi Shaun, Thanks for reporting this, I have just committed the fix. I will let you know if we add the read_name to the truncated output. -K On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __**_ 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/ ___ 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] value_label tool input param attribute doesn't work as documented
Hi Leandro,
I tested this on my instance and the example you gave did give me the
correct string: Human (hg18). Do you still have this problem? If so, can you
provide an example where it still behaves incorrectly?
Thanks,
K
On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi,
Looking at the example on the Tool Config Syntax wiki page:
Example
Assume that the tool includes an input parameter named database which is
a select list ( e.g., assume the following inputs ):
Toggle line
numbershttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#
1
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_1
inputs
2
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_2
param format=tabular name=input type=data label=Input stuff/
3
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_3
param type=select name=database label=Database
4
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_4
option value=alignseq.loc*Human (hg18)*/option
5
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_5
option value=faseq.locFly (dm3)/option
6
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_6
/param
7
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b4282c0f9aa2576fbdec6550c3174f_7
/inputs
Assume that the user selects the first option in the $database select
list. Then the following will ensure that the tool produces a tabular data
set whose associated history item has the label Blat on *Human (hg18)*.
Toggle line
numbershttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#
1
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_1
outputs
2
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_2
data format=input name=output label=Blat on
${database.value_label} /
3
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e84df1d17f7b92455ff66b9d18618b_3
/outputs
It shows that .value_label attribute should produce the string in between
the option tags, not the actual value.
Why does this not work? When I use it it produces the value, or am I doing
something wrong?
regards,
Leandro
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Re: [galaxy-dev] checkboxes bug fix
Hi L-A, I tried this on today's tip but could not reproduce the bug. I added your param param name=SQA type=boolean label=Run SolexaQA checked=true / to a tool and the correct value was produced on the command line and in the configfiles block as well. Re-running also gave the correct result. Are you still seeing this problem? Thanks, K 2011/8/15 Louise-Amélie Schmitt louise-amelie.schm...@embl.de Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A __**_ 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/ __**_ 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/ ___ 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/ ___ 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] Sam2interval.py bug
The read_name has been implemented as well. Thanks, K On Wed, Aug 24, 2011 at 1:15 PM, Kanwei Li kan...@gmail.com wrote: Hi Shaun, Thanks for reporting this, I have just committed the fix. I will let you know if we add the read_name to the truncated output. -K On Tue, Aug 2, 2011 at 6:54 AM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __**_ 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/ ___ 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] Setting the output label based on input parameters?
Hi Nikhil, The tool templates are Cheetah templates, so you can do things like: outputs %if param == True: data format=txt name=blah label=Label1 / %else data format=txt name=blah label=Label2 / %endif /outputs Thanks, K On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote: Hi all, Is there a way to set the label of the output based on the input parameters? Perhaps by using the action tag? Basically, I want the output label to be different if the user sets a particular parameter to be true. - Nik. ___ 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/ ___ 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] Extracting regions of sequences given table of co-ords
Done On Fri, Aug 12, 2011 at 5:36 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Aug 11, 2011 at 4:11 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: *The tool should work with general fasta files right now, so the changes needed to support protein and other fastas should be UI-based only. Right, while of course preserving the (now misleading) tool ID of Extract genomic DNA 1 and filename of extract/extract_genomic_dna.xml for backwards compatibility. Only the tool ID is required for backwards compatibility; the filename can be changed. OK. First, some minor house keeping - if you can clarify the text for how a user should go from a tabular file to an interval or GFF file, that would be good: https://bitbucket.org/peterjc/galaxy-central/changeset/d41ee8c41532 Could you transplant/merge that please? Its the only commit so far on my new branch: https://bitbucket.org/peterjc/galaxy-central/src/extract_region Regards, Peter ___ 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/ ___ 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] workflows are broken in current galaxy-central version
Fixed on trunk, thanks for reporting! K On Thu, Jul 21, 2011 at 12:41 PM, Edward Kirton eskir...@lbl.gov wrote: URL: https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8 Module paste.exceptions.errormiddleware:*143* in __call__ Module paste.debug.prints:*98* in __call__ Module paste.wsgilib:*539* in intercept_output Module paste.recursive:*80* in __call__ Module paste.httpexceptions:*632* in __call__ Module galaxy.web.framework.base:*145* in __call__ https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#body *=* method*(* trans*,* kwargs *)* Module galaxy.web.framework:*84* in decorator https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#* return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.web.controllers.workflow:*686* in editor https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#* return* trans*.*fill_template*(* workflow/editor.mako*,* stored*=*stored *,* annotation*=*self*.*get_item_annotation_str*(* trans*.*sa_session*,* trans*.*user*,* stored *)* *)* Module galaxy.web.framework:*661* in fill_template https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#* return* self*.*fill_template_mako*(* filename*,* kwargs *)* Module galaxy.web.framework:*672* in fill_template_mako https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#* return* template*.*render*(* data *)* Module mako.template:*296* in render https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8#* return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8# _kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8# _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*) * Module mako.runtime:*718* in _exec_template https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8# callable_*(*context*,* ***args*,* kwargs*)* Module _base_panels_mako:*87* in render_body https://galaxy.jgi-psf.org/workflow/editor?id=3918559ba2a747d8# __M_writer*(*unicode*(*self*.*overlay*(*visible*=*self*.*overlay_visible*) **)**)* *TypeError: render_overlay() got an unexpected keyword argument 'visible'* ___ 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/ ___ 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] Pull request for Galaxy
Hi Nick, Thank you! Although there was a tiny error in there with base_panels ;) For the future, yes, please shoot an email to galaxy-dev and either create a bitbucket issue with the patch, or have a link to the pull request. Thanks, K On Tue, Jul 19, 2011 at 11:25 AM, Nick Semenkovich seme...@alum.mit.edu wrote: Hi -- I just submitted a tiny first pull request for some minor Galaxy changes (to correct wiki links): https://bitbucket.org/galaxy/galaxy-central/pull-request/2/update-galaxy-wiki-links (Not sure if I should e-mail the dev list about these or what. How do these get approved?) Thanks! Nick -- Nick Semenkovich 314.374.4434 Medical Scientist Training Program School of Medicine Washington University in St. Louis http://web.mit.edu/semenko/ ___ 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/ ___ 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] removing Select All / Unselect All buttons from a set of check boxes
Hi Hans, I have created a ticket at BB: https://bitbucket.org/galaxy/galaxy-central/issue/614/remove-the-select-all-and-unselect-all Sorry for the late reply. Thanks, K On Sat, May 7, 2011 at 9:02 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Is there a way to remove the Select All and Unselect All buttons from a set of check boxes? - crated with: param name=samples type=select display=checkboxes multiple=true dynamic_options=ds_samplesFromServer()/ I have a very long list, and I don't want to encourage people to tick all boxes. Thank you very much for your help, Hans ___ 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/ ___ 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] empty status for non-empty datasets
Hi Shantanu, Thanks for the report. Is there any pattern to the files being marked as empty? Certain filetype or histories? -K On Mon, Jul 11, 2011 at 3:07 PM, Shantanu Pavgi pa...@uab.edu wrote: Hi, In our local galaxy install (currently revision 50e249442c5a) we are seeing few output datasets as 'empty' in the galaxy web interface. The actual file size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by clicking on download/view icons, however they can't be imported in other workflows. I looked into the database and figured out that file_size column value for corresponding dataset id is zero. I am guessing that's why it is being shown as empty in the web interface. Any suggestions on how to resolve this will be helpful. -- Thanks, Shantanu. ___ 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/ ___ 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] Saved Histories - default view on deleted histories (bug)
Hi Michal, Can you elaborate on set on deleted items by default? It is always active by default for me. Thanks, K On Wed, Jul 6, 2011 at 3:23 AM, Michal Stuglik michal.stug...@gmail.com wrote: hi all, in galaxy-central: 1. default view in Saved Histories section is set on deleted items ( Jeremy, I did double check this morning on fresh instance :)) 2. in advanced search option: one of the filter switch is deleted and does the same job as active switch 3. Sugestion: Saved Histories-Advanced Search sharing: private | shared | accessible | published | all deleted: active | deleted | all maybe it is better to change it to: sharing: private | shared | accessible | published | all status: active | deleted | all I think deleted is not clear.. all the best, michal ___ 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/ ___ 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] BAM display at Trackster
Is this from a recent changeset that you pulled? On Wed, Jul 6, 2011 at 2:19 PM, Vipin TS vipin...@gmail.com wrote: Hi Galaxy team, I am experiencing a problem with visualizing my BAM files through Trackster at my Galaxy instance. Please find the attached image along with this mail. From the log file I am not seeing any clues about the error message which is displayed on my browser page (A dependency (bai) was in an error state.) I updated my instance recently, It will be great if you can help me on the same. Thanks in advance, Vipin Friedrich Miescher Laboratory of the Max Planck Society Tuebingen ___ 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/ ___ 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] Fwd: Request for pulling the updated FASTQ (de-)interlacer tool
Committed on trunk. On Thu, Jun 2, 2011 at 2:25 AM, Florent Angly florent.an...@gmail.comwrote: Hi Kanwei, I think we'll get more feedback once it when it is added to Galaxy. I have run small tests (included in the functional tests) and real large datasets and have had no issues with the scripts and wrappers. Regards, Florent On 27/05/11 18:49, Kanwei Li wrote: Has anyone on the list tried this patch? Feedback would be appreciated. Thanks, K On Fri, May 27, 2011 at 1:27 AM, Florent Angly florent.an...@gmail.comwrote: Can anyone comment on my email please? Florent On 22/05/11 14:03, Florent Angly wrote: Let me know if you have any questions about this. Thanks, Florent Original Message Subject: Request for pulling the updated FASTQ (de-)interlacer tool Date: Tue, 17 May 2011 17:47:13 +1000 From: Florent Angly florent.an...@gmail.com florent.an...@gmail.com To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edugalaxy-dev@lists.bx.psu.edu Dear Galaxy team, Please consider pulling these changes I made to the interlacer/de-interlacer tools into the main Galaxy repository:https://bitbucket.org/fangly/galaxy-central/changeset/7f7ec8f05d36 While the tools were handling mate pairs fine, I now added the ability to also keep single reads (reads that miss their mate) in a separate file. The functional tests were updated and pass. Thanks, Florent ___ 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/ ___ 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] Galaxy BLAST XML to tabular fix
Sorry, it slipped by. Committed! On Wed, May 25, 2011 at 12:48 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, May 18, 2011 at 6:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Kanwei, Could you merge this branch or transplant this fix please? https://bitbucket.org/peterjc/galaxy-central/changeset/3c0b903c86a9 https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_05_18 New branch, blast_2011_05_18 There is no change to the logic, just to the assert statement where the sanity test didn't consider doubly masked sequences. Should I also update the XML wrapper's version number as well? Thanks, Peter Hi Kanwei, Did this email reach you? Let me know if you want a new unit test to go with it and/or to bump the tool's version number. Regards, Peter ___ 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] new galaxy-dist fixes multiple IE UI bugs
Thank YOU for reporting them ;) On Wed, May 25, 2011 at 11:33 AM, Leandro Hermida soft...@leandrohermida.com wrote: Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE, for e.g. the workflow editor works now works and the history expand/collapse works! :) ___ 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/ ___ 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] Problem with file's extension
Hi Shashi, You can add your own datatypes using the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes Thanks, K On Wed, May 25, 2011 at 1:05 PM, shashi shekhar meshash...@gmail.comwrote: Hi All, I have some problem with extension of file.some executables file will recognize the only the specific extension like autodock . it takes one input file ( extension with .dpf ) and one outpt file (extension with .dlg). how can we resolve such type of problem . Regards Shashi shekhar ___ 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/ ___ 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] Reciprocal Best Hits (RBH) from BLAST tabular output
Hi Peter, I think the tool shed would be appropriate for this... -K On Tue, May 17, 2011 at 6:23 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, May 4, 2011 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I mentioned just over a month ago that I had written a Galaxy tool to do find Reciprocal Best Hits (RBH) from BLAST tabular output or similar (e.g. Bill Pearson's FASTA tabular output). http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004825.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-April/004829.html The only problem I had was setting default columns, which I consider to be a minor bug in Galaxy: https://bitbucket.org/galaxy/galaxy-central/issue/507 Regardless of this small usability issue, would the Galaxy team like to add this tool to the main distribution (to sit along with my BLAST+ wrappers), or should I submit it to the tool shed? If you want to merge it, the following change set should suffice: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 I made a subsequent change set to test giving column defaults as value=c2 rather than value=c2 which makes no difference, but if this is how default column values are meant to be given, take this change too: https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30 A third commit fixes a typo in the help: https://bitbucket.org/peterjc/galaxy-central/changeset/2be6c0bc76ea Would the Galaxy team like to merge this tool into the trunk (and if so, do you have any suggestions for improvements or changes), or should I put it up on the Galaxy Tool Shed instead? Thanks, Peter ___ 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] problem running latest galaxy-central
Hi Assaf, Nate has just committed a fix so this shouldn't be required now. Thanks for the report! K On Thu, Apr 28, 2011 at 4:28 PM, Assaf Gordon gor...@cshl.edu wrote: I'll rephrase my question: Is cython going to be a standard requirement for Galaxy (and needs to be manually installed on our production servers), or is this just a temporary thing, or is it going to be an automatic egg thing ? WATSON Mick wrote, On 04/28/2011 04:11 PM: Looks like it :) http://cython.org/#download From: galaxy-dev-boun...@lists.bx.psu.edu [ galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Assaf Gordon [ gor...@cshl.edu] Sent: 28 April 2011 20:52 To: galaxy-...@bx.psu.edu Subject: [galaxy-dev] problem running latest galaxy-central Question: The recent galaxy-central revision ( 2b057869b72f ) doesn't work on my computer, saying DistributionNotFound: cython=0.12.1. Example: $ hg clone http://bitbucket.org/galaxy/galaxy-central/galaxy_hidden_dataset_test $ cd galaxy_hidden_dataset_test $ hg id 2b057869b72f tip $ sh run.sh ... ... ... Traceback (most recent call last): File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/buildapp.py, line 81, in app_factory from galaxy.app import UniverseApplication File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/app.py, line 11, in module from galaxy.tools.imp_exp import load_history_imp_exp_tools File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/tools/imp_exp/__init__.py, line 6, in module from galaxy.web.base.controller import UsesHistory File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/web/base/controller.py, line 12, in module from galaxy.visualization.tracks.data_providers import get_data_provider File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/visualization/tracks/data_providers.py, line 11, in module pkg_resources.require( pysam ) File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py, line 404, in require return c[req.project_name].require() File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py, line 237, in require dists = self.resolve() File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /home/gordon/temp/galaxy_hidden_dataset_test/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /home/gordon/temp/galaxy_hidden_dataset_test/lib/pkg_resources.py, line 565, in resolve raise DistributionNotFound(req) # XXX put more info here DistributionNotFound: cython=0.12.1 = I'm running debian/stable, with Python 2.6.6 (r266:84292, Dec 26 2010, 22:31:48) Do I need to install something (cython) ? -gordon ___ 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/ ___ 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/ ___ 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] MarkupSafe egg cannot be fetched
Thanks, fixed on trunk On Sat, Apr 23, 2011 at 7:05 PM, Edward Kirton eskir...@lbl.gov wrote: hello, after pulling the latest changes from galaxy-central, i get the following error: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched $ python scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched ___ 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/ ___ 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] BLAST+ HTML output broken
K On Tue, Apr 19, 2011 at 11:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote: 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 ___ 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] update probelm...
Hi Liisa, What does hg tip return? K On Mon, Apr 11, 2011 at 10:55 AM, Liisa Koski liisa.ko...@dnalandmarks.ca wrote: Hi I just tried to update my local installation of Galaxy but accidentally hit Ctr-C when it asked me a question added 285 changesets with 649 changes to 354 files local changed static/scripts/packed/jquery.jstore.js which remote deleted use (c)hanged version or (d)elete? interrupted! When I tried to do the update again...it says 'no changes found' But...after restarting my instance...I see that the changes did not get implemented. Is there a way to force this? Thanks in advance, Liisa ___ 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/ ___ 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] PostgreSQL issue: reserved keyword used as identifier
Hi Louise, Have you considered doing a SQL dump and import? Sounds easier to me than writing a perl script ;) -K 2011/4/8 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Le vendredi 08 avril 2011 à 11:12 -0400, Sean Davis a écrit : 2011/4/8 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello everyone I just met a huge problem concerning the database. I'm currently trying to transfer my data from MySQL to PostgreSQL by writing a Perl script that would do the job. Here is the issue: In the form_definition table, one of the field identifiers is desc, which is a reserved SQL keyword used for ordering values. Therefore, There's currently no way of making any query of the type INSERT INTO table_name (identifiers list) VALUES (values list); which is a big handicap in this context, since the order of the identifiers list we dynamically retrieve is not necessarily (and seldom) the right order. Is there a way to fix this issue without blowing everything up? You need to quote the identifiers. A simple example using desc as a column name: sdavis=# create table test_table( id int, desc varchar); ERROR: syntax error at or near desc LINE 3: desc varchar); ^ sdavis=# create table test_table( id int, desc varchar); CREATE TABLE Hope that helps. Sean Thanks, but I cheated by duplicating a little the information and it works fine. I use insert into table values (...);. I still have problems transfering the data though. The script runs without growling but nothing is actually written in the target tables... I'll have to see that on monday now :/ If I succeed, I'll let you know. Cheers, L-A ___ 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/ ___ 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] Password input field for tools?
Hi Daniel, I have attached a patch that does this below. You can use it by setting param type=password However the security is lacking as you can see the string when you try to re-run the job and view source. Is this sufficient for your purposes? Thanks, K On Sat, Apr 2, 2011 at 11:01 AM, Daniel Schmidt danielschmid...@gmx.net wrote: Hi all! Is there any way to use password input fields (input type=password...) with tools? A tools XML definition file only seems to support text and textarea fields. I already tried setting a tools parameter type to password, which unfortunately results in an Unknown tool parameter type 'password'. Trying password=True (like area=True) does not result in an error, but the text field is still just a normal text field. I may be mistaken, as I am new to Python and Galaxy, but there already seems to be a PasswordField class and a TextField class, which both can be found in several files. Was the PasswordField class for tool parameters maybe disabled for a reason? Thanks! Daniel ___ 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/ passwordparam.patch Description: Binary data ___ 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] Updating BLAST+ wrapper
Done the manual way ___ 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] History information popup broken on library entries?
Thanks for reporting this. I will improve the popups next week as they are giving people lots of issues. On Fri, Mar 18, 2011 at 12:05 PM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi all, I've been exploring how to use Galaxy's shared library functionality, and have noticed that once imported into a working history, that the little 'i' information icon's black popup window isn't working for these datasets. All it says is 'Could not find the job for this dataset.' This appears to affect multiple file types (FASTA and BAM tested) and both files copied into Galaxy or linked to at import. I'm using the current latest code from galaxy-central, https://bitbucket.org/galaxy/galaxy-central/changeset/e39495db6071 This also seems to affect http://test.g2.bx.psu.edu/ and also http://main.g2.bx.psu.edu/ Can anyone confirm this behaviour? I'm using Firefox on the Mac, but I doubt that is relevant. Peter ___ 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/ ___ 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] [galaxy-user] Peep view for history elements broken on IE?
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has
all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
Peter
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Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?
Hi Peter, The changes are on tip, which aren't in galaxy-dist or on main yet. I will look into the other issues when I get access to my IE7 VM tomorrow. Thanks! K ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?
All: I retested under IE7 and found the bugs you were mentioning. This has all been fixed on trunk by using a newer local storage library. The only IE7 issue that I am now aware of is when the tool pane is empty when using workflows. Please let me know if you see any other issues. Thanks, K On Mon, Jan 31, 2011 at 1:06 PM, Peter pe...@maubp.freeserve.co.uk wrote: On Mon, Jan 31, 2011 at 5:54 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, In IE go to Tools - Internet Options - Advanced Tab, then under Browsing section: Uncheck Disable Script debugging (Internet Explorer) Uncheck Disable Script debugging (Other) Check Display a notification about every script error Then you will see the Javascript error when you try to reload the Galaxy page and then try to expand a history item. I would help debug the Galaxy IE issues but I am at work and cannot change these settings on my work computer (the are grey out :( ) -Leandro I had done Disable Script debugging (Internet Explorer) and Display a notification about every script error, but not Disable Script debugging (Other). However I still don't see any javascript error when using Galaxy. Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu 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/
Re: [galaxy-dev] NCBI BLAST+ wrappers in Galaxy?
Committed On Tue, Feb 1, 2011 at 10:27 AM, Peter pe...@maubp.freeserve.co.uk wrote: Hi Kanewi, Sorry - make that three changesets on this branch to consider mering/transplanting: https://bitbucket.org/peterjc/galaxy-central/changeset/blastplus_jan31 Parameter handling, https://bitbucket.org/peterjc/galaxy-central/changeset/aa82d8273063 Cope with errors on stderr, https://bitbucket.org/peterjc/galaxy-central/changeset/1bd227e7eb4c Ensure blast jobs get killed, https://bitbucket.org/peterjc/galaxy-central/changeset/607b7268693a Peter ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
