Re: [galaxy-dev] cufflinks libz error/warning
Hi all - I'm running Galaxy on my Redhat linux cluster. When I run cufflinks from the shell I get the error/warning: cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks) but it still seems to run ok. It looks like Galaxy is choking on this. I tried compling cufflinks manually but that was more troublesome. Is there a way I can get Galaxy to ignore this error and continue? Ryan, There's currently no way to tell Galaxy to ignore some error messages and not others; we're working on this functionality but it's far from being done*. Unfortunately, your best bet is to compile Cufflinks on your system. FYI, here's a technical description of this problem: http://seqanswers.com/forums/showthread.php?t=8042 *To detect particular errors, we envision XML elements in a tool's output definition that use regular expressions to identify errors amongst a program's output. We think this is the right approach, but we haven't started implementing it yet. You are welcome to do so; we welcome code contributions from the community. Thanks, J. ___ 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] Missing Page Editor Components
However, when I tried to use the Edit Pages function, there is no Embed Galaxy Object and Insert Link to Galaxy Object in the Page Editor. I have set the enable_pages = True in universe_wsgi.ini. Wonder what else can cause the problem? Charlie, This bug has been fixed in galaxy-central changeset r5231:642f1f9e5e3a Also, is there any documentations for the control syntax used in datatypes and tools configure xmls? Datatypes: https://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes Tool config: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Best, J. ___ 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] cufflinks libz error/warning
It looks like the output only occurs when cufflinks can't run on the provided dataset. I checked my inputs, and I think that is the problem...its a sam file from bowtie, not from tophat, hence not a sorted sam file. Perhaps this stderr message doesn't matter after all, its just misleading... Yes, I think you are correct. Let us know if you have more questions. Best, J. ___ 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 trying to download workflow
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export it
successfully, so updating your Galaxy instance may solve your problem. If not,
let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists rather than
individual galaxy developers for community and archival purposes; I've cc'd
this one to galaxy-dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the galaxy-dev
list (http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
when trying to download a workflow.
Were you able to find a solution or are you still working on it? I attached a
screenshot of the workflow (like you also requested on the list). Let me know
if I can provide you with any additional details to help with the debugging.
Best regards,
Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] GET
/workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1 500 -
http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07;
Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
file:///home/diehl/Pictures/Screenshot.png
Fedora/3.6.16-1.fc14 Firefox/3.6.16
Error - type 'exceptions.TypeError': 'WorkflowStep' object is
unsubscriptable
URL:
http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in
__call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 74 in
decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4,
sort_keys=True )
File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line
1078 in export_to_file
stored_dict = self._workflow_to_dict( trans, stored )
File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line
1571 in _workflow_to_dict
step['inputs'].append( { name : name, description : runtime parameter
for tool %s % module.get_name() } )
TypeError: 'WorkflowStep' object is unsubscriptable
Screenshot.png
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Re: [galaxy-dev] Question about cuffcompare tool implementation
Assaf, Assuming cuffcompare generates a TMAP and REFMAP file for each input file, does this mean the wrapper tool retrieves only the first and second input files' TMAP and REFMAP files ? Yes, this is the way it works currently. This is clearly problematic, but it meets most users' needs as it enables them to generate a file of combined transcripts--which is needed for Cuffdiff--from many sets of Cufflinks' transcripts. Currently, the Galaxy framework isn't set up to generate multiple outputs for each input; I'm not sure how difficult it will be make these extensions, and it hasn't been a priority as users haven't voiced a need for these files. Of course, contributions are always welcome if you put something together. Best, J. and others are ignored ? Or is there some galaxy black magic python code that iterates multiple inputs and imports them all ? ___ 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 trying to download workflow
Thanks Sarah. I was having trouble reproducing because I hadn't set a runtime
parameter. I've fixed the bug in galaxy-central changeset 5387:835656900dd0 ;
after making this change, I was able to successfully export and import
workflows with runtime parameters.
Best,
J.
On Apr 14, 2011, at 10:01 AM, Sarah Diehl wrote:
I could narrow it down even further. As soon as I set anything to To be set
at runtime the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose download fails. I recreated
the workflow at the public instance at http://main.g2.bx.psu.edu and
shared it with you. There the download also fails for me.
Best regards,
Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not,
you'll have to do some debugging yourself. Here are some things you
might try:
*on your local instance, try exporting simpler workflows and seeing if
there's a tool or configuration that does or does work.
*on our public instance, try creating a workflow identical to the one
that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance
that I have access to, I can probably fix it.
Thanks,
J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the
workflow still does not work. The error is the same.
Best regards,
Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export
it successfully, so updating your Galaxy instance may solve your
problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists
rather than individual galaxy developers for community and archival
purposes; I've cc'd this one to galaxy-dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the
galaxy-dev list
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
when trying to download a workflow.
Were you able to find a solution or are you still working on it? I
attached a screenshot of the workflow (like you also requested on
the list). Let me know if I can provide you with any additional
details to help with the debugging.
Best regards,
Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] GET
/workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1 500 -
http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07;
Mozilla/5.0
(X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
fil
e:///home/diehl/Pictures/Screenshot.png
Fedora/3.6.16-1.fc14 Firefox/3.6.16
Error -type 'exceptions.TypeError': 'WorkflowStep' object is
unsubscriptable
URL:
http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
145 in __call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
line 74 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ),
indent=4, sort_keys=True )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1078 in export_to_file
stored_dict = self._workflow_to_dict( trans, stored )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1571 in _workflow_to_dict
step['inputs'].append( { name : name, description : runtime
parameter for tool %s % module.get_name() } )
TypeError: 'WorkflowStep' object is unsubscriptable
Screenshot.png
___
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and other Galaxy lists, please use the interface at:
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___
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and other Galaxy lists, please use the interface at:
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___
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Re: [galaxy-dev] Email notification and Workflow sharing for all users
Paul, Sorry for the slow reply. We've been discussing this issue internally: 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? Published workflows should meet your needs as they are accessible to all users. What we think should happen--but isn't yet implemented--is that published workflows should appear below shared workflows when a user clicks Workflows -- All Workflows. We plan to implement this in the future, but it's not a priority right now. If you do implements something of this sort, please consider share your code either by forking on bitbucket or sending a patch to this list; we welcome community contributions to the galaxy source code. Best, J. ___ 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 problem
Olen, This is a runtime error, not an update error; it is occurring because we mistakenly committed code that is not compliant with python 2.4 Here are your options to fix this error: (1) update your python version from 2.4 to 2.5 or 2.6; (2) update your installation from galaxy-central; specifically, you'll need changeset 5370:1cb94990d839 (3) make the changes in changeset manually: https://bitbucket.org/galaxy/galaxy-central/changeset/1cb94990d839 and then merge when the next update comes out. Sorry for the inconvenience. J. On Apr 18, 2011, at 5:58 PM, Olen Vance Sluder Jr wrote: 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 update.out___ 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] question about Filtering Cufflink files
Hello, This is a bug and has been fixed. I reran your analyses on our test server and they completed successfully, so you should be good to go. Best, J. On May 3, 2011, at 6:08 AM, shamsher jagat wrote: Jeremy, I have been trying to follow the steps in filtering Cufflink out put files you have described in one of the previous messages (http://gmod.827538.n3.nabble.com/Re-downstream-analysis-of-cuffdiff-out-put-td2836457.html): I have shared histroy with you, but in summary: File 35: when Filter GTF data by attributes value list on data 11 (combined GTF) and data 33 (which is gene expr file) . Will not this should have one gene per row. But it is not? File 39: Filter GTF file by attribute value list on data 11 and data 38 (Cuffdiff splicing expr) it failed. I would assume that it should filter on the basis of TSSid . The error message is Traceback (most recent call last): File /var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py, line 67, in filter( gff_file, attribute_name, ids_file, output_file ) File /var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py, line 57, in filter if attributes[ attribute_name ] in ids_dict: KeyError: 'tss_id' 40 : Filter GTF data by attribute list on data 11 and 34 (tss group exp) failed and error message is: Traceback (most recent call last): File /var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py, line 67, in filter( gff_file, attribute_name, ids_file, output_file ) File /var/opt/galaxy/g2test/galaxy_test/tools/filters/gff/gtf_filter_by_attribute_values_list.py, line 57, in filter if attributes[ attribute_name ] in ids_dict: KeyError: 'tss_id' I would consider that if one gene has different Id than there is splicing . However in contrast isoform file with transcript Id is working fine (File 20) On a different note can I convert GTF file to txt tab delaminated file I tried to convert file 11 in txt (following Edit attributes) but the file is not properly formatted especially col-pid and TSS id. Am I doing something wrong. Thanks. ___ 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 of cufflinks
Sarah, We recently updated the Cufflinks/compare/diff wrappers to be compatible with v1.0.* ; the wrappers are available in galaxy-central and should be available in galaxy-dist in the next couple weeks as we're planning another release soon. New features in v1.0.* have not been implemented in these updates (and, in fact, there are features from 0.9.* that are still not available); the changes we made were simply to ensure that the wrappers' current functionality works with the new versions. In the next couple months we plan to extend the current wrappers to include new functionality. However, community contributions that extend the current wrappers to include new functionality would be most welcome, and we can integrate them into the galaxy code base if/when they are available. Best, J. On May 10, 2011, at 7:53 AM, Sarah Diehl wrote: Hello everybody, I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version? 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] Update of cufflinks
Thanks Assaf. A couple notes on Galaxy's Cufflinks' wrappers and update checks: *galaxy-central changeset 4557:eee0e1d344d2, which updated the Cufflinks/compare/diff wrappers to support v1.0.* disabled the update check for Cufflinks. *There is no --no-update-check option for for Cuffcompare; I haven't checked to see if Cuffcompare actually contacts cufflinks.cbcb.umd.edu before running or not. *galaxy-central changeset 5638:1ab3dfb5d929 disables the update check for Cuffdiff. Best, J. On Jun 2, 2011, at 3:33 PM, Assaf Gordon wrote: Just FYI, With the recent version of cufflinks (at least 1.0.2), the developers added a 'feature' of automatic version check. While the idea is nice, the implications are not: cufflinks,cuffcompare and cuffdiff will connect to host cufflinks.cbcb.umd.edu every time you run them. I'm sure the intentions were good, but I don't like programs calling home, basically reporting usage statistics and origins. The check_update code is also not written with security in mind, and might be exploited (buffer overruns and such) - it's best to disable it. This will also generate a message to STDERR, which is just annoying (and bad, with galaxy). To disable it on the command line, add --no-update-check to every invocation. If you compiled it from source code, edit the file ./src/common.cpp and change the line: bool no_update_check = false; to: bool no_update_check = true; Then recompile and re-install. -gordon Jeremy Goecks wrote, On 05/10/2011 09:02 AM: We recently updated the Cufflinks/compare/diff wrappers to be compatible with v1.0.* ; the wrappers are available in galaxy-central and should be available in galaxy-dist in the next couple weeks as we're planning another release soon. New features in v1.0.* have not been implemented in these updates (and, in fact, there are features from 0.9.* that are still not available); the changes we made were simply to ensure that the wrappers' current functionality works with the new versions. In the next couple months we plan to extend the current wrappers to include new functionality. However, community contributions that extend the current wrappers to include new functionality would be most welcome, and we can integrate them into the galaxy code base if/when they are available. Best, J. ___ 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] question/bug with cuffcompare wrapper
Assaf, Thanks for the very helpful information. We largely sync our tool wrappers to the tool version used on our public server. We're currently running v1.0.1 of Cufflinks on main; hence, as you discovered, the wrappers are compatible with that version of Cufflinks but (sadly) incompatible with newer versions. If you modify the Cufflinks/compare/diff wrappers to be compatible with 1.0.2/3, please either put them in the toolshed or send them to me and I'll incorporate them into the Galaxy code base. Thanks, J. On Jun 6, 2011, at 2:42 PM, Assaf Gordon wrote: Hi, It seems the cuffcompare XML wrapper expects a file named cc_output to contain the transcript accuracy report. I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2, this file is now named cc_output.stats, and the transcript accuracy file is empty. so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 (Unless I missed something in the XML/python/cuffcompare execution chain). Also, Notice that starting version 1.0.2 they've added an option to normalize by either total number of reads or by number of reads that matched the given GTF file. To make matters worse, cufflinks defaults to normalizing to total reads, and cuffdiff defaults to normalizing by GTF-matching reads. The options are called --total-hits-norm and --compatible-hits-norm. There's no way for users to specify either of those in Galaxy, so running cufflinks/cuffdiff might give unexpected results (not that there are any expected results, but still...) Just something to think about when you work on the next version of cufflinks wrappers. -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/
Re: [galaxy-dev] CuffDiff output mis-named ?
Based on the naming convention of the other outputs (and the output files from cuffdiff), I think the label of the first one should be renamed to CDS Expression only (assuming the relevant input file cds_exp.diff). Correct. That said, I've been planning to reorder and rename the Cuffdiff outputs for a while now; changes in are galaxy-central changeset 5650:dc97d0a852cb Thanks, J. ___ 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/
[galaxy-dev] Fwd: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw
John, Questions about local installs are best directed to galaxy-dev, so I've moved the question to this list. While executing cuffcompare, I encountered this error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. how should i solve this problem? thanks a lot! A recent change set has made Cuffcompare compatible with v1.0.3: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 You'll need to update your Galaxy instance with this change set for Cuffcompare to work; also note that the change set is in galaxy-central, not galaxy-dist. Best, J.___ 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/
[galaxy-dev] Fwd: a Trackster Question
Matt, I'm moving your Trackster question onto the galaxy-dev list: one issue I keep running into is that it's not super clear how to go about configuring the dynamic tracks you showed off in your talk. Is there some guidance somewhere that I am missing on this? I confess my own motive is to be able to dynamically interact with a sliding window-based algorithm for measuring DNA replication status from sequencing data. This would help us parameterize the algorithm before running it on the entire data set. This (very new) galaxy-central changeset: https://bitbucket.org/galaxy/galaxy-central/changeset/a7e9af183746 formalizes tool integration into Trackster. To enable the Show Tool option in Trackster for a particular tool, two things need to happen: (a) add the trackster_conf/ tag to the tool XML file; (b) ensure that the tool has parameters supported by Trackster; only integer, float, and static select parameters are currently supported in a tool's interface, but it is straightforward to add support for other parameter types as well, and we'll do so as needed. We'll create a wiki page soon so that this information is easier to find. Let us know if you have more questions. Best, J. ___ 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
Yes, all BAM fails are failing with the same error message. Before updating my instance I did not try to visualize through Trackster. Samtools path are available to Galaxy. I am not seeing any error/warning message in my log file. Try this in the main interface: (1) click the pencil on a BAM dataset; (2) try converting from BAM to BAI; If the conversion failed, you should receive an informative error message about why it's failing. Once you get this conversion to pass, you should be able to visualize your BAM dataset in Trackster. Let us know if you're still having trouble. Best, J. ___ 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] Multiple fastq files per forward/reverse mates (tophat and related tools)
I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files. Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag. Gus, if you end up modifying the Tophat wrapper to support multiple input datasets, please submit a patch or fork galaxy-central via bitbucket and I'll integrate these enhancements into the Galaxy code base as this would be nice functionality to have. Best, J. ___ 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] Multiple fastq files per forward/reverse mates (tophat and related tools)
Gus, Good to hear about your progress. Please send me a patch of your changes and I'll take a look. You can create a patch using Mercurial from the command line as follows. % hg diff tophat.patch Thanks, J. On Jul 13, 2011, at 7:37 PM, W. Augustine Dunn III wrote: First off thank you heartily for pointing me in the right direction here. It SEEMS like i have managed to accomplish this. Meaning: i finally got the run to get past the parsing of the config file and now have a process running on the cpu and the server log shows a command line string that matches what I was trying to get. However I am VERY new at the whole Cheetah craziness, so I DEF want you folks to double check my work. I would LOVE to contribute a patch but have these questions and concerns: I cloned the 'dist' branch not the 'central' branch originally and am not sure if my tophat_wrapper.xml version will clash with any that have been included in the central branch, I would assume that the system's diff capabilities SHOULD be able to sort this out but I am WAY more familiar with git than hg. I have created a bitbucket account and supplied my pubkey, but I dont see anything on the wiki that describes how a person gets push or similar permissions on the galaxy project what is the procedure for correctly submitting these types of piecemeal single file changes? Thanks again for your help and I am very excited to have a chance to give back! Gus On Mon, Jul 11, 2011 at 8:51 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files. Sarah's suggestion is spot on. See the Cuffcompare wrapper for an example of how to use this tag. Gus, if you end up modifying the Tophat wrapper to support multiple input datasets, please submit a patch or fork galaxy-central via bitbucket and I'll integrate these enhancements into the Galaxy code base as this would be nice functionality to have. Best, J. -- In science, fact can only mean confirmed to such a degree that it would be perverse to withhold provisional assent. I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. -Stephen Jay Gould ___ 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] Newer Version of Cufflinks Wrapper
Ilya, Despite the wrapper version numbers (which I'll update shortly to avoid further confusion), the current Cufflinks wrapper in both galaxy-central and galaxy-dist supports Cufflinks v1.0.3 However, not all new options for v1.0.3 are implemented the current wrappers; should you decide to implement additional options in the Cufflinks/compare/diff wrappers, please consider submitting a patch that we could incorporate into Galaxy. Best, J. On Jul 21, 2011, at 1:30 AM, Chorny, Ilya wrote: Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics – Intern icho...@illumina.com 858-202-4582 ___ 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
It turns out there sort of is, extract/extract_genomic_dna.xml However, as written it isn't clear to me how to make this work with general tabular files, and how it would behave with proteins (which in principle can be process the same way). It also appears to insist on having both start and end present (I want to be able to have these default to the start/end of the referenced parent sequence). Peter Any thoughts from the Galaxy team? Are you open to making extract/extract_genomic_dna.xml more general - for instance renaming and rewording to indicate work on protein FASTA files as well as nucleotide FASTA files and reference genomes (assuming it does work)? Peter, We're open to enhancing this tool. Here are my thoughts: *Enabling the tool to work with general tabular formats would seem to be a relatively low priority because it's easy to convert a general tabular file into a simple BED file by cutting columns. If you plan to support a general tabular format, the GOPS tools provide examples of how to work with BED, GFF, and interval datasets. *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. Best, J. ___ 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] Updated Cufflinks Wrapper
Hi Ilya, Thanks for the contribution; most of it has been committed in changeset 0ef81af1de09 A couple notes: *I couldn't transplant your changes because your commit did not include recent changes to the Cufflinks wrapper. It appears you didn't merge correctly with the main repository at some point; please try to merge correctly as it speeds up the inclusion process significantly on our end. *I didn't include your changes to the Tophat wrapper because merging was incorrect and I couldn't figure out what you were trying to do. Let us know if you have any questions. Best, J. On Jul 27, 2011, at 7:26 PM, Chorny, Ilya wrote: I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D. Bioinformatics – Intern icho...@illumina.com 858-202-4582 ___ 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] Extract Genomic DNA insisting on build for GFF3 file
Actual result: Red error against the gff file, Unspecified genome build, click the pencil icon in the history item to set the genome build The fact I'm using a FASTA file from my history should mean the genome build is irrelevant as that only applies to locally cached genomes (right?). Correct. Fixed in galaxy-central changeset 07de40a5a0b9 Thanks, J. ___ 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] trackster reference genome
Colin, How is it possible to preinstall a reference genome for trackster (hg19) within galaxy. i tried to find a dedicated help page but could not find any. Could you please link me to relevant information? See the section titled 'Setup for local instances' on this page: http://wiki.g2.bx.psu.edu/Learn/Visualization Finally, please send all emails to our mailing lists--in this case, galaxy-dev, which I've cc'd--rather than individual Galaxy developers or other list members. Sending email to the mailing lists ensures that everyone can see and contribute to questions and issues; in addition, emails to mailing lists are tracked and archived so that they are available in the future. Best, J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
Great. Could you try that example on the latest galaxy-central please? I have revision 06f0bca6de24 and get the following error using the steps given earlier: Traceback (most recent call last): File /home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py, line 261, in if __name__ == __main__: __main__() File /home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py, line 128, in __main__ chrom = feature.chrom AttributeError: 'Header' object has no attribute 'chrom' Fixed in galaxy-central changeset 3c7416baa157 Best, J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
I think I've found another problem in exploring possible workarounds, 1. Goto http://usegalaxy.org (or a local Galaxy running galaxy-dist or galaxy-central) 2. Import this GFF3 file, ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.gff 3. Click on the pencil for this dataset to Edit Attributes 4. Under Convert to new format, Convert GFF to Interval Index, convert Expected result: New interval file Actual result: Traceback (most recent call last): File /home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py, line 39, in main() File /home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py, line 26, in main for feature in list( reader_wrapper ): File /home/pjcock/repositories/galaxy-central/lib/galaxy/datatypes/util/gff_util.py, line 213, in next group = interval.attributes.get( 'group', None ) AttributeError: 'Comment' object has no attribute 'attributes' Fixed in galaxy-central changeset 3c7416baa157 Best, J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
Well, sort of. After converting that GFF3 file into BED, the strand column isn't set in the metadata. That seems important! We'll look into this. Also a point of clarification, I had the wrong URL for the FASTA file. This is the whole genome, although to actually proceed with this example, the sequence must be renamed to just NC_005213.1 rather than the NCBI's gi|38349555|ref|NC_005213.1| in order to match the naming in the GFF file. ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.fna Correct. J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
However, the FASTA output uses different names because it embeds the start/end co-ordindates as is. Thus using GFF3 features, the sequence name includes _883_2691_ while using BED features the same sequence has instead _882_2691_ for its name. I propose this be harmonised by always using one-based counting in the FASTA names (as done in GFF files but also GenBank, EMBL, etc) rather than the convention used in BED files (and Python) which is confusing to most non-programmers. i.e. I suggest this change (with new tests to enforce it), https://bitbucket.org/peterjc/galaxy-central/changeset/e7393df0fbc1 Peter, I have concerns about this change. IMO, the goal of embedding the start/end coords in the fasta name is to (a) embed important information from the input file into the fasta name and (b) make it simple for users to connect a fasta sequence to an entry in the interval file. These goals are achieved with the current code _relative to the input file_. This connection between the input and output files key. However, in the case of a user using a mix a BED and GFF files for a single genome, your concern becomes an issue. In practice, I don't think we've seen users encounter this issue yet, which leads to me think that the current code is fine. One idea to address both of these issues is to embed the original format in the fasta name so that it's clear whether the coords are BED or GFF (e.g. hg17_BED_chr1_147962192_147962580). Best, J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
Sorry -more questions - could you explain what the Interpret features when possible setting in the Extract Genomic DNA is meant to do? The tool's help text doesn't say anything (other than it is only for GTF/GFF files). In the NC_005213.1 example turning Interpret features when possible on seems to massively collapse down the number of features. I'm not sure what is happening but suspect this is in part down to the NCBI GFF3 file being broken with regards to the lack of any ID tags? See also: http://blastedbio.blogspot.com/2011/08/why-are-ncbi-gff3-files-still-broken.html Peter, Interpret features means that the GFF parser aggregates features for a single parent feature (i.e. does multi-line parsing), extracts the sequences for each child feature, and creates the sequence for the parent by concatenating the child features' sequences. Yes, this needs to be better documented. And on another issue, looking at the code for extract_genomic_dna.py there appears to be no attempt to support circular genomes with features wrapping the origin. Correct, this is not implemented. J. ___ 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] Extract Genomic DNA insisting on build for GFF3 file
One idea to address both of these issues is to embed the original format in the fasta name so that it's clear whether the coords are BED or GFF (e.g. hg17_BED_chr1_147962192_147962580). Or hg17_gtf_chr1_147962192_147962580 etc. That certainly seems better than the current situation. However, my preferred solution is to take the FASTA ID from the annotation file. In GFF3 this would be the ID tag in column nine (if present), perhaps with an option to use another custom tag like locus_tag or transcript_id if preferred. Hi Peter, This seems reasonable. Of course, the implementation needs to be done with care to (a) ensure the default choice is somewhat similar to what is done now and (b) support all flavors of GFF. If you choose to implement this, you'll also need to update all the existing test output files. For BED I had initially thought this would the optional column 4, name. This made me wonder what Galaxy is doing in converting GFF3 to BED, since column 4 was populated with generic feature types (gene, CDS, etc from GFF3 column 2). Shouldn't this be using the feature's ID tag (if present)? Yes, I'd say that's correct. The GFF-to-BED converter was written before we had GFF parsing support, and at the time it wasn't possible to extract the name from the attributes. Finally, note that all changes made to any GFF code must work for GFF, GFF3, and GTF formats. Thanks, J. ___ 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] trackster problem with IE8 and IE7 when using June 23, 2011 release
Hi Hans, We haven't done much testing of Trackster with IE yet, and I wouldn't be surprised if it's broken because IE doesn't follow standards in many important areas. Trackster should work with Chrome, Safari, and Firefox in all cases. We'll continue to work to improve Trackster functionality in IE. To help us, it would be useful if you could open the Javascript console and report the error(s) you see when trying to run Trackster to the galaxy-bugs mailing list. Best, J. On Aug 19, 2011, at 7:45 AM, Hans-Rudolf Hotz wrote: Hi I am sorry to be a pain in the neck, but as part of our quarterly upgrade procedure, I am stumbling across the next problem: Can anybody confirm, that the visualization does not work with the June 23, 2011 release (changeset: 5743:720455407d1c) when using IE8 or IE7 on windows XP? (it works with chrome and firefox6 on windows XP, and no problems with mac and linux) And like the previous problems, is there a quick fix available? Thank you very much for your help Regards, 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] filtering BED files by score in trackster
The option to filter a BED file by the score in the visualization tool is brilliant! There is just one draw back: you can only filter by integers. Hence a score of 1.1 is the same as of score of 1.3. How difficult would it be to change the code in order to allow floats for the filter? Such a feature would help us a lot! Hi Hans, Good catch. The actual filtering step is fixed in galaxy-central changeset 5943:4f992059bfeb However, right now the slider/text still works in whole numbers most of the time; I'm not sure if it's feasible to have it work in tenths by default because that creates a huge number of possible slider states. If you didn't know, you can type in numbers to the slider labels, but that too rounds right now--this should probably be changed. Can you share a BED file with floats in the score column and I can play with it a bit? Thanks, J.___ 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] cuffcompare wrapper
I'm confused. Why would the symlink cause problems for Cuffcompare but not for other tools that use symlinks (including Cufflinks and Cuffdiff)? J. On Sep 8, 2011, at 1:43 PM, Chorny, Ilya wrote: It’s not an issue in the tmp dir but in the job_working_directory. I run most of those other tools with no problems. I don’t think we should make it a requirement across the board and I think we can come up with alternative ways to clean up the job_working_directory. I am hoping that you could add the symlink to the cuffcompare wrapper as it is the only one where the symlink causes me a problem as far as I have tested. We don’t want to have our code base differ to much from galaxy-central. Thanks, Ilya From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Wednesday, September 07, 2011 6:26 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cuffcompare wrapper Ilya, A search of the Galaxy codebase indicates that thirteen tools use symlinks (e.g. GATK, Sicer, Picard, Cuff*, Bowtie), so the changes required to support this new code are significant. (Changes would also likely be needed for tools in the tool shed.) Also, asking tool wrappers to delete symlinks would be an idiosyncratic requirement as tools assume they have a temporary working directory at their disposal. For these reasons, it seems best to have the tool framework clean up symlinks as necessary to support the new code. Best, J. On Sep 7, 2011, at 2:28 PM, Chorny, Ilya wrote: Ok, I figured out why you need the symlink. Can you add an unlink after the process completes? i.e for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.unlink(input_file_name) From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Wednesday, September 07, 2011 9:18 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] cuffcompare wrapper Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for i, arg in enumerate( args ): input_file_name = ./input%i % ( i+1 ) os.symlink( arg, input_file_name ) cmd += %s % input_file_name My code: for i, arg in enumerate( args ): cmd += arg Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: icho...@illumina.com Website: www.illumina.com ___ 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] Loading Histories etc
Hi Shaun, I have built up a large collection of Galaxy data on my local account and I am now finding the following operations very slow: Showing saved histories I just committed a fix in galaxy-central that should help out considerably: https://bitbucket.org/galaxy/galaxy-central/changeset/7850b1df5d39 Let us know if you continue to have problems here. Refreshing a history containing many data items Opening a library with ~200 files These are known issues that we plan to work on in the future; however, we're not actively working on them right now. I am using a mysql database. Would postgres help? I am yet to see a reliable way of converting between mysql and postgres so haven't done this yet. Changing databases is unlikely to speed up performance much; the bottleneck is in the python/mako code. Thanks, J. ___ 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] Data transfer between two galaxy instances
Len, This a beta feature with multiple usability issues. That said, it should work; here's how: Galaxy provides a URL when you export a history; take note of this URL as this is the one that you'll when importing the link. If Galaxy doesn't provide a link, update the history somehow (e.g. change its name slightly) and Galaxy will provide the URL again. Another catch: you'll need to make the history 'accessible via link' for the URL to work. You can do this via Options -- Share or Publish menu. Good luck, J. On Sep 27, 2011, at 6:07 PM, lenta...@jimmy.harvard.edu lenta...@jimmy.harvard.edu wrote: Hi Hans (and all), Thank you for the recommendation. I wasn't even aware of this feature--it is exactly what our site needs. But I have yet been able to successfully transfer a history this way. I've tried various permutations of importing/exporting to/from our site and galaxy (http://main.g2.bx.psu.edu/), but everytime I click submit on the Import from File page, nothing seems to happen. My history is a small test-set containing two trivial files so it should transfer over immediately. Sometimes when I click on the Export to file button, my browser downloads a tar-ball. But I can't submit this tarball on the import from file page because it expects a URL. I was wondering if there are other devs out there who might be able to replicate my bug. It would help me to determine if it is something specific to our deployment, or whether this might be a galaxy bug. If you've been able to get Export to/Import from file to work for your site *recently* I'd love to talk to you! Thanks, Len For those who are interested, the link generated for my http://cistrome.org/ap/history/export_archive?id=e529b88352bf9863 Hi Have you tried the 'Export to File' followed by 'Import from File' for individual histories? This worked for us very well, at least for small histories with small data files associated with them a few months ago. Regards, Hans On 09/23/2011 09:26 PM, lenta...@jimmy.harvard.edu wrote: Hi, We are running two instances of galaxy on our site--one internal, the other external. Some of our internal users have data on the external instance. What might be the easiest way to transfer the data of our internal users from the external to the internal instance? OR Is there a way to transfer data between galaxy instances? I thought that I'd give this mailing list a shot before telling our internal users that they would have to re-load the data on the internal instance. Thanks, Len Taing ___ 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] Bug in cufflinks_wrapper.xml?
Curt, You are correct, this is a bug. It was fixed in this changeset: https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60 We'll be updating galaxy-dist in the next week and this change will be available then. Thanks, J. On Oct 5, 2011, at 5:54 PM, Curt Palm wrote: I have been having trouble getting cufflinks to run with the -g or -G parameters via Galaxy. when I select either use reference annotation or use reference annotation as guide from the pulldown menu, cufflinks runs , but the -g or -G is not added to the cufflinks command. I think I have found the problem in the cufflinks_wrapper.xml file. line17#if $reference_annotation.use_ref == use reference annotation: line18-G $reference_annotation.reference_annotation_file line19#end if line20#if $reference_annotation.use_ref == use reference annotation guide: line21-g $reference_annotation_guide.reference_annotation_guide_file . line56 conditional name=reference_annotation line57param name=use_ref type=select label=Use Reference Annotation line58option value=NoNo/option line59option value=Use reference annotationUse reference annotation/option line60option value=Use reference annotation guideUse reference annotation as guide/option line61/param note that Use is capitalized in lines57 and 59 but not in lines 17 and 20. I made these changes in lines 17,20 and 21 and I now get the -G and -g are passed to the cuffflinks command use to Use in lines 17 and 20 reference_annotation_guide.reference_annotation_guide_file to reference_annotation.reference_annotation_guide_file in line 21 line17#if $reference_annotation.use_ref == Use reference annotation: line18-G $reference_annotation.reference_annotation_file line19#end if line20#if $reference_annotation.use_ref == Use reference annotation guide: line21-g $reference_annotation.reference_annotation_guide_file -curt *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ 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/
[galaxy-dev] hardware for local galaxy install
David, Please direct questions about local installations to the galaxy-dev mailing list (cc'd); there are a large number of experienced people of this list that can likely help with this and similar questions. Just a quick question about the compute infrastructure of the setup running the public instance of Galaxy. Our Galaxy copy is on our High Performance Cluster here at X and they are currently canvassing users about the next upgrade of the HPC. This cluster serves the needs of all the university academics here and so we are sharing time with physicists, aerodynamics engineers etc. However, the HPC board of directors tell me that they see biological computing problems as the next big growth area for them - especially now we have a copy of Galaxy. What they would like to know is what kind of mix of new nodes would be most useful to us. They have about X million pounds to spend (about X million dollars) and the question as I understand it is determining the right mix of expensive high memory nodes (e.g. with 1 or 2TB RAM on board) and cheaper lower memory nodes (e.g. with 32G ram on board or less even). The problem for me is that I have no idea what to suggest (I am not that compute savvy). So any advice from your experiences (or that of the Galaxy team) would be most helpful. Your hardware will depend on what types of analyses you plan to support/run. For instance, assembly jobs (e.g. ABySS, Velvet, Trinity) require high-memory nodes, and read mapping jobs (e.g. BWA, Bowtie, Tophat) are best run on high CPU nodes. Also, creating indices (often used in visualization) such as bigWig and bigBed require large amounts of memory as well. You'll want to do some research on the tools that you plan to run most often and determine the best hardware for them. Nate Coraor's presentation at GCC 2011 has some useful information about setting up a production Galaxy as well as details about our public instance: http://wiki.g2.bx.psu.edu/Events/GCC2011 In short, we use multiple clusters to distribute resource-intensive jobs appropriately. Also, you may want to search the galaxy-dev mailing list as there's been discussion about hardware specs for a Galaxy instance previously: http://gmod.827538.n3.nabble.com/Galaxy-Development-f815885.html Nate and others, please feel free to chime in with additional information. Good luck, J. ___ 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] Some changes to tophat and cufflinks wrappers for indexing loc files
I made some changes to the cufflinks and tophat wrapper to pull gtf files from an indexed loc file as opposed to from history. The diff’s are attached. I made it an optional feature. Please let me know if this makes its way into galaxy-central. Ilya, This looks like a good start. A couple questions: (1) Do you have a sample GTF indices file similar to e.g. bowtie_indices.loc.sample ? (2) Would it be useful to provide GTF index files in Cuffcompare, Cuffdiff, and Tophat as well? Thanks, J. ___ 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] Version String
Shaun, version_command is what you want: version_commandtophat --version/version_command A couple things to note: *tool path isn't needed if the tool is in your galaxy user's path; *your tool must have a --version command line option; if not, you'll have to modify the command. This functionality should be working as of latest Galaxy dist. If you're still having trouble, it would be useful to try running a tool with a known, functioning version command (e.g. Tophat, Bowtie, Cufflinks/compare/diff) and seeing if it produces the version as output. Let us know if you're still having problems. Thanks, J. On Oct 13, 2011, at 5:42 AM, SHAUN WEBB wrote: Hi. I am using the tag: version_stringpath to tool --version/version_string In my xml file. I would expect the tool version to be printed in the information window for each dataset but the version field is blank. I am running the latest Galaxy dist, is there anything else I need to do? I have tried using version_command also. Thanks Shaun -- 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] Importing Historys in other Galaxy instances
Hi Ross, I checked the following: wget link works, I can download the file. It's not saved as Historyname.tar.gz but as export_archive?id=a69ee3e00cb4d02c. Anyway, I can unpack the archive with tar xfvz. hg head: Änderung:5955:949e4f5fa03a Marke: tip Nutzer: Nate Coraor n...@bx.psu.edu Datum: Mon Aug 29 14:42:04 2011 -0400 Zusammenfassung: Missing import in library_contents.py Where can I find the file (I assume?) paster.log? Best place to look for the error is in the job table. Try this query for your database: -- select id, state, command_line, stdout, stderr from job where tool_id='__EXPORT_HISTORY__' order by id desc; -- and look at the stderr column for some information about the problem. Please send us the command line and the stderr for the problematic jobs; this should help us figure out what's going on. Thanks, J. ___ 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] Importing Historys in other Galaxy instances
-- select id, state, command_line, stdout, stderr from job where tool_id='__EXPORT_HISTORY__' order by id desc; -- The query should actually be: select id, state, command_line, stdout, stderr from job where tool_id='__IMPORT_HISTORY__' order by id desc; Thanks, J. ___ 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] cufflinks version
David, Wrapper supports v1.0.0 to v1.1.0 I'll update the wiki momentarily. J. On Nov 2, 2011, at 2:04 PM, David Hoover wrote: What version of cufflinks do the current Galaxy wrappers support? The wiki (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies) says 1.0.1, but our local instance only works with 1.1.0. Can the wiki be updated? David Hoover Helix Systems Staff http://helix.nih.gov ___ 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] Local galaxy Cufflinks problem
Chris, The problem is likely a bug in the Cufflinks wrapper that was recently fixed in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60 Try updating your Galaxy instance to include this changeset; if this doesn't fix the problem, let us know. Good luck, J. On Nov 11, 2011, at 10:44 AM, Bidwell, Christopher A. wrote: Colleagues, We have set up a local Galaxy but I am having trouble running Cufflinks with the annotation gtf file. We have the iGenomes btau4.2 genome in the database and use the iGenomes btau4.2 gtf file in the history. However the –G isn’t showing up in the command line (below) and the output is the same as when I run cufflinks without annotation. Is something not set up correctly? Info: cufflinks v1.0.3 cufflinks -q --no-update-check -I 5 -F 0.05 -j 0.05 -p 4 -N -b /phillip/hiscansq/run00085-09-16-11_D0D1KACXX/110916_H179_0062_AD0D1KACXX/hr00206_OAR13-24/References/Bos_taurus/genome.fa The details page shows the gtf file being supplied from the history Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 26: Tophat for Illumina on data 2 and data 1: accepted_hits Max Intron Length 5 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Aonnotation24: Btau42_iGenomes_annot.gtf Conditional (bias_correction) 0 Conditional (seq_source) 0 Conditional (singlePaired)0 Thanks for your help. Chris ___ 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] Broken published history in a local installation
Nico, Does this happen when publishing new histories or just for histories that have been published previously? If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well. J. On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote: Hi all, Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration. Thanks for any pointers, Nico --- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delho...@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --- Screen shot 2011-11-17 at 13.56.18.pngATT1.txt___ 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] Broken published history in a local installation
Nico, That's odd. I can't reproduce your issues on my local instance using that rev. We're releasing a new dist in the next week; the simplest thing is do is hope that updating to the new dist fixes the problem. If not, let me know and we'll try something else. Best, J. On Nov 17, 2011, at 9:22 AM, Nicolas Delhomme wrote: Hi Jeremy, That's occuring for both. I'm pulling from galaxy-dist (sorry, my mistake). It's our production environment that we've updated a couple of weeks ago. To look up the tip, I just ran an 'hg summary' in the galaxy root directory: [galaxy@ouzhou galaxy]$ hg summary parent: 6056:338ead4737ba tip Nico --- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delho...@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --- On 17 Nov 2011, at 14:59, Jeremy Goecks wrote: Nico, Does this happen when publishing new histories or just for histories that have been published previously? If you're pulling from galaxy-central, you're running a very old version of Galaxy. Currently tip is 6292:9b7d5c1c0be6 ; updating your instance to tip may solve the problem as well. J. On Nov 17, 2011, at 8:00 AM, Nicolas Delhomme wrote: Hi all, Since the last pull from galaxy-central (6056), whenever I try to access published histories, I get a file not found error; see the attached screenshot. I have not changed any configuration. Thanks for any pointers, Nico --- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delho...@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --- Screen shot 2011-11-17 at 13.56.18.pngATT1.txt___ 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] Question about from_work_dir
Aurelien,
The particular behavior that you need isn't currently supported because the
value of from_work_dir isn't treated as a template. To work around this
limitation, you can do the move/copy operations in your tool wrapper; see the
wrappers for Bowtie and Sicer for examples on how to do this.
Good luck,
J.
On Nov 28, 2011, at 12:21 PM, Aurélien Bernard wrote:
Hi everybody,
I'm currently trying to create a wrapper for one of my program.
This program generates several output file and the name of each output file
is derived from the name of the main input file.
In the .xml file I try to get my output files with the following tag:
outputs
data from_work_dir=${input_file}.out label=${input_file} main output
format=txt /
...
/outputs
The corresponding input file tag:
param name=input_file type=data label=Input label format=alr
help=Requested file type: ALR /
The problem is that the content of the from_work_dir attribute is not
interpreted by galaxy (Contrary to the label attribute) and therefore I get
this error message:
galaxy.jobs DEBUG 2011-11-28 17:44:24,431 finish(): Could not move
/home/galaxy/galaxy-dist/database/job_working_directory/326/${input_file}.out
to /home/galaxy/galaxy-dist/database/files/000/dataset_684.dat as directed by
from_work_dir
Do I made a syntax error ? Do I misunderstand the function of the
from_work_dir attribute ?
Thank you in advance for your help.
Best regards,
Aurélien Bernard
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Re: [galaxy-dev] Can't view data files from published histories, only imported histories
Liisa, I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly: http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 (Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.) Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way? J. On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks jeremy.goe...@emory.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, This functionality works fine in some instances, e.g. for this history: http://main.g2.bx.psu.edu/u/cartman/h/repeats I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history? Thanks, J. On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following. Error - type 'exceptions.NameError': global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined If I import the history into my own history pane I can click on the eye and see the data with no errors. Any ideas how I can see the data from the published histories? Thanks, Liisa Liisa Koski Bioinformatics Programmer ___ 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] Question about from_work_dir
Aurelien, The particular behavior that you need isn't currently supported because the value of from_work_dir isn't treated as a template. To work around this limitation, you can do the move/copy operations in your tool wrapper; see the wrappers for Bowtie and Sicer for examples on how to do this. Good luck, J. Hi Jeremy, Is it possible to build the required string elsewhere in the .xml file using cheetah and then pass the resulting string like from_work_dir=$result or is using a wrapper really the only way to go? I'm writing a config for a tool that names the output files using the options, so I could potentially concatenate the option values to get the required file name if I could do that. Alex, The best approach is for your tool to accept output file names; then, in the command_line tag of the tool wrapper XML, you can build the output name based on options chosen by the user. Finally, please always cc the mailing list for community and archival purposes. Thanks, J. ___ 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 core services vs wrapper.py duplication caching of .fai files
Curtis, [curtish@cheaha galaxy]$ find . -name *.py | xargs grep sam_fa_indices.loc ./tools/samtools/sam_pileup.py:seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR ... ./tools/ngs_rna/cufflinks_wrapper_without_gtf.py: cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) Is there any place in galaxy-core where such a core service lives and could be used by all these adaptors, rather than replicating the code everywhere? Not yet, but this is definitely needed. However, tools and Galaxy must remain independent , so the location of needed indices should be passed to the tool via the command line rather than having tools call into Galaxy. As a related question, for fasta genomes from the current history, these wrappers compute the .fai file on the fly, in TMP, then throw it away, every time. Has there been any discussion about storing such derived indices in the dataset’s metadata (like the .bai file on a .bam data set), so it gets computed once, then re-used? Converted datasets, which subsume indices-as-metadata, can store dataset indices. Extending converted datasets to store indices created on the fly is also very much needed. Any community contributions that address these issues would be most welcome. Best, J.___ 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] extract_genomic_dna.py checks alignseq.loc?
Hi Holger, I went to the respective file and found that the line which defines seq_file is commented out: (l.38 in def check_seq_file()) ## seq_file = %s/alignseq.loc % GALAXY_DATA_INDEX_DIR This seems to be a bug in the current version of the file. There is clearly something amiss. In the galaxy-dist source, this line is not commented: https://bitbucket.org/galaxy/galaxy-dist/src/b258de1e6cea/tools/extract/extract_genomic_dna.py Removing the comment, the script tries to check for sequence entries in alignseq.loc, which I left empty before, since I didn't need aligned sequences in galaxy until now. Of course this results in another error: 'No sequences are available for 'hg19', request them by reporting this error.' This is the correct behavior. I just wanted to raise the question if this dependency is right, wouldn't one rather like to check for the respective build in faseq.loc (unfortunately the file format is different, it doesn't contain the seq in the first column). Yes, faseq.loc should be used. The use of alignseq.loc is a historical artifact that we haven't fixed yet. If you're inclined to fix it, we'd be happy to incorporate the changes into the code base. Best, J. ___ 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] Can't view data files from published histories, only imported histories
Liisa, Updating FastQC won't solve this issue. You'll need to manually update galaxy-dist with this changeset to see the graphs: https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea Otherwise, you can wait until the next galaxy-dist to get this changeset. Best, J. On Nov 30, 2011, at 2:39 PM, Liisa Koski wrote: Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks jeremy.goe...@emory.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 14:46 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly: http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 (Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.) Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way? J. On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks jeremy.goe...@emory.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa
Re: [galaxy-dev] [galaxy-bugs] Problem with indexing a genome through tophat on a local copy of Galaxy...
Hi David, There should be additional information in the galaxy database about why the job failed; take a look at stderr column of the failed job using some SQL like this: -- select * from job where state='error' and tool_id='tophat' and stderr like '%indexing reference%' order by id desc; -- If that doesn't work, try something simpler: -- select * from job where state='error' and tool_id='tophat' order by id desc; -- What are the errors that you see? Finally, please direct future questions about local Galaxy installations to galaxy-dev (cc'd) so that the community can learn from and participate in discussions. Thanks, J. On Dec 5, 2011, at 10:09 AM, David Matthews wrote: Hi, We have a local version of Galaxy here at Bristol and it is very nice. However, it does not like to run TopHat on large genomes (i.e. Human) but is happy with small ones (e.g. viruses). The genome we have is hg19 but missing chr Y and this genome works fine on the PSU version. However, we seem to be hitting a wall when we run it here and it seems to relate to the indexing part right at the begining. Here is the error output we see in the red box: An error occurred running this job:Settings: Output files: /tmp/tmppA7Hrk/dataset_942.*.ebwt Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt m And here is the stuff we see when we click on the green bug (the second set is just the last bit of a long list of stuff): Error indexing reference sequence Returning block of 520230381 Getting block 6 of 7 Reserving size (531691900) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:59 Sorting block of length 346541282 (Using difference cover) Sorting block time: 00:06:04 Returning block of 346541283 Getting block 7 of 7 Reserving size (531691900) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:40 Sorting block of length 408062248 (Using difference cover) Sorting block time: 00:07:08 Returning block of 408062249 Exited Ebwt loop fchr[A]: 0 fchr[C]: 837200431 fchr[G]: 1417119193 fchr[T]: 1997326330 fchr[$]: 2835690133 Exiting Ebwt::buildToDisk() Total time for backward call to driver() for mirror index: 01:16:32 TopHat v1.2.0 We are running on our HPC and have directed the job to land on a whole node with 8GB of ram on board. Any ideas why the index is failing? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk ___ 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-bugs] Problem with indexing a genome through tophat on a local copy of Galaxy...
David, There are many steps in Tophat, only some of which can be parallelized. Hence, utilization appears low in many instances when Tophat is doing a step that cannot be parallelized. I'm not aware of anything that can be done to optimize Tophat further, but you could contact the Tophat authors and ask for their suggestions: tophat.cuffli...@gmail.com If you find anything that works well, please share it with the list. Good luck, J. On Dec 6, 2011, at 4:55 AM, David Matthews wrote: Hi Jeremy, Many thanks for this, I'll pass it over to our HPC guys to work on it (my grasp of this is a bit flimsy). On a related note. When tophat is running on one of our nodes it seems to be very slow and when we check the activity on the node we typically see that is is using about 6.8GB of ram and about 16.5 GB of virtual memory with about 1% CPU activity - presumably because there is a lot of I/O which slows down the run. Is this roughly what you would expect on an 8GB node? Each node is 8GB RAM and 1GB RAM per core. Anything we can do at this end to optimise this a bit? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk On 5 Dec 2011, at 21:00, Jeremy Goecks wrote: Hi David, There should be additional information in the galaxy database about why the job failed; take a look at stderr column of the failed job using some SQL like this: -- select * from job where state='error' and tool_id='tophat' and stderr like '%indexing reference%' order by id desc; -- If that doesn't work, try something simpler: -- select * from job where state='error' and tool_id='tophat' order by id desc; -- What are the errors that you see? Finally, please direct future questions about local Galaxy installations to galaxy-dev (cc'd) so that the community can learn from and participate in discussions. Thanks, J. On Dec 5, 2011, at 10:09 AM, David Matthews wrote: Hi, We have a local version of Galaxy here at Bristol and it is very nice. However, it does not like to run TopHat on large genomes (i.e. Human) but is happy with small ones (e.g. viruses). The genome we have is hg19 but missing chr Y and this genome works fine on the PSU version. However, we seem to be hitting a wall when we run it here and it seems to relate to the indexing part right at the begining. Here is the error output we see in the red box: An error occurred running this job:Settings: Output files: /tmp/tmppA7Hrk/dataset_942.*.ebwt Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt m And here is the stuff we see when we click on the green bug (the second set is just the last bit of a long list of stuff): Error indexing reference sequence Returning block of 520230381 Getting block 6 of 7 Reserving size (531691900) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:59 Sorting block of length 346541282 (Using difference cover) Sorting block time: 00:06:04 Returning block of 346541283 Getting block 7 of 7 Reserving size (531691900) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:40 Sorting block of length 408062248 (Using difference cover) Sorting block time: 00:07:08 Returning block of 408062249 Exited Ebwt loop fchr[A]: 0 fchr[C]: 837200431 fchr[G]: 1417119193 fchr[T]: 1997326330 fchr[$]: 2835690133 Exiting Ebwt::buildToDisk() Total time for backward call to driver() for mirror index: 01:16:32 TopHat v1.2.0 We are running on our HPC and have directed the job to land on a whole node with 8GB of ram on board. Any ideas why the index is failing? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk ___ 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 web interface falls over when running TopHat
David,
What is the full stack trace that you're seeing? The stack trace is the text
below Traceback and identifies the exact location where the problem occurs.
Are you following these guidelines:
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
for setting up large genomes in Galaxy?
Also, it would be ideal if you could upload the problematic data--genome +
reads--to our public instance (main.g2.bx.psu.edu) and see if you can reproduce
the problem that you're seeing.
Thanks,
J.
On Dec 9, 2011, at 12:20 PM, David Matthews wrote:
Hi,
We seem to have sorted out the problem of TopHat failing to run but now we
have a new problem. When TopHat runs with a large genome (but not with small
genomes), it finishes the run fine and all the data is there but the web
interface falls over about 8 hours into the run and when we try to access the
web based interface we get a Proxy Error. When we restart it all looks fine.
This is the sort of errors our HPC people find:
Exception happened during processing of request from ('XXX.XXX.XXX.XXX',
32960)
Traceback (most recent call last):
File
/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/pa
ste/httpserver.py, line 1053, in process_request_in_thread
Unexpected exception in worker function lambda at 0x201caed8
Traceback (most recent call last):
File
/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/pa
ste/httpserver.py, line 863, in worker_thread_callback
Unhandled exception in thread started by bound method Thread.__bootstrap of
Th
read(worker 118, stopped 1127647552)
Traceback (most recent call last):
Do you have any suggestions for what is happening?
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.
Tel. +44 117 3312058
Fax. +44 117 3312091
d.a.matth...@bristol.ac.uk
___
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Re: [galaxy-dev] How and where to install tool dependencies
Josh, It appears that there are shell directories for the tools under ~/galaxy-dist/tools/ with basic wrapper scripts but without the corresponding executables (very few that I've noticed have the tools already in them). Is the intent to download the dependency tools and (building from source if necessary) take the binaries in those directories and copy them to their corresponding directory under ~/galaxy-dist/tools/? This seems to have worked with an error I first got when clipping a FASTQ file which reported that fastx_clipper was not a recognized command. So I downloaded the FASTX Toolkit, compiled the binaries, and copied only the binaries into the corresponding fastx tools directory. Would I do the same thing for TopHat and Cufflinks by taking all their binaries (combined) and copying them into ~/galaxy-dist/tools/ngs_rna/? You'll want to read about Galaxy Tool files a bit to understand the files in ~/galaxy-dist/tools: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#Admin.2BAC8-Tools.2BAC8-Tool_Config_Syntax.Galaxy_Tool_XML_File These are not shell directories; instead, they include tool config files + additional wrapper scripts to run a tool in Galaxy. To answer your question, executables for tools need to be in your path but do not need to be in the config/wrapper directories. For example, in an SGE cluster, we suggest setting the PATH environment var in ~/.sge_request Even if that is the case though, I have occasionally gotten errors about tools missing in completely different directories. One was for the FASTQ Groomer. One user saw this error in their browser (which for now is the only way I know to figure out where tools are *expected* to be): File /home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFastQC.py error - cannot find executable /home/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc The exception to the above is Java-based tools. For these tools, you'll need to use the ~/galaxy-dist/shared/jars directory. This is a limitation of Galaxy that will likely be addressed in the future. Adding a brief page on the Galaxy wiki site under the Admin section about this would really help, even if it only showed an example for one or two specific tools. I looked a bit but couldn't find it; I suspect it is out on the wiki somewhere, though clearly it needs to be easier to find. Good luck, J. ___ 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] Hidden history item
Alex, I just implemented this functionality in galaxy-central changset 303741fda0ec and documented it on the wiki. https://bitbucket.org/galaxy/galaxy-central/changeset/303741fda0ec http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set Best, J. Hi all, by default I let my tools produce (the old way) a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden=true in the output tag but that does not make any difference. Is this possible at all or only applicable to running workflows? Any pointers appreciated. 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/
Re: [galaxy-dev] embedded code into Pages
I would like to modify Pages a lot. For example, I would like to create a galaxy Page with rss-reader written in PHP (or javascript) in it. I found where content is stored for Pages, but not the script who read this content. Pages uses the WYMEditor to render Pages: http://www.wymeditor.org/ See the wym*.[css/mako/html] and jquery.wymeditor.js files for details. Is there any possibility to integrate code into Galaxy Page which could be executed ? It's not clear exactly what you're looking to do, but Pages includes JS code to load histories/datasets/workflows on expansion. You might look there as a starting point for executing code in Pages. Let us know if you have more questions. Good luck, J. ___ 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] Written tutorial
Jeff, The screencasts are in place of written tutorials; we've received feedback in the past that screencasts are often easier to understand and use. We'll try to locate the datasets used in these tutorials. Thanks, J. On Dec 29, 2011, at 9:43 AM, Rosenfeld, Jeffrey wrote: Hi Jeremy, Thank you for the link. I have already seen those files, but I was hoping for written instructions and the files for the video tutorials. Jeff On 12/29/2011 09:19 AM, Jeremy Goecks wrote: Jeff, Here are some tutorials on basic NGS analyses in Galaxy: http://main.g2.bx.psu.edu/u/james/p/exercises Best, J. On Dec 22, 2011, at 11:54 AM, Rosenfeld, Jeffrey wrote: Hi, I am trying to teach some people to use Galaxy, and I was looking for a written tutorial that went through the basics of taking sequence reads, gromming and trimming them and then doing alignment. I see that you have this type of exercise as screencasts: http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service , but this is not something written where users can follow instructions and do it themselves. Also, there is no indication as to where to download the example files used in the screencasts. Thanks, Jeff ___ 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] Written tutorial
Jeff, Here are some tutorials on basic NGS analyses in Galaxy: http://main.g2.bx.psu.edu/u/james/p/exercises Best, J. On Dec 22, 2011, at 11:54 AM, Rosenfeld, Jeffrey wrote: Hi, I am trying to teach some people to use Galaxy, and I was looking for a written tutorial that went through the basics of taking sequence reads, gromming and trimming them and then doing alignment. I see that you have this type of exercise as screencasts: http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service , but this is not something written where users can follow instructions and do it themselves. Also, there is no indication as to where to download the example files used in the screencasts. Thanks, Jeff ___ 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] defining genome assembler in galaxy
Top and qstat are generic unix utilities for tracking jobs. Running 'man command' will, assuming they are installed on your system, provide the best information for using them. J. On Dec 29, 2011, at 12:09 PM, Bassam Tork wrote: Dear Jeremy, Thank You very much, I will try your suggestion. Could you please guide me to the link/webpage that talks about checking the job manually using top/qstat/similar. Happy New Year, Bassam Tork. On Thu, Dec 29, 2011 at 9:18 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: My idea was to pass all above including main.bash as parameters to the python wrapper (called run.py, attached), as follows: where the last parameter sys.argv[7] is the output file, specified by xml file. This is the correct approach. But galaxy was running for more than 3 hours, although it should take only 7-10 minutes on our server with no results. Vispa should write its output to dataset_192_I_2_20_CNTGS_DIST0_EM20.txt , where dataset_192 .txt is the reads file.But dataset_192_I_2_20_CNTGS_DIST0_EM20.txt did not appear in galaxy-dist/database/files/000. run.py: simply coppies data from dataset_192_I_2_20_CNTGS_DIST0_EM20.txt to galaxy output file, but nothing is coppied since dataset_192_I_2_20_CNTGS_DIST0_EM20.txt was not created. How could the results appear?Could somebody help me ? The first thing to check is if run.py functions correctly outside of Galaxy. If so, try checking the job manually using top/qstat/similar system utilities to figure out where the job is stuck. Good luck, J. ___ 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] (OperationalError) unable to open database file
The manual highly recommend postgresql, is there any critical point to use it, instead of mysql? I am just more familiar with mysql. Thanks. The Galaxy team has found that, when running Galaxy, postgres is more stable and robust than mysql. Also, we use postgres ourselves, so it's easier for us to aid with debugging. Best, J. ___ 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] Make Galaxy continue running when i close the browser
Efthymois, You'll want to run Galaxy as a daemon process. Run % sh run.sh --help to get more information on running Galaxy as a daemon. Also, please direct questions about running/configuring a local Galaxy instance to galaxy-dev (cc'd) rather than galaxy-user, which is for tool and analysis questions. Best, J. On Jan 5, 2012, at 8:06 AM, Makis Ladoukakis wrote: Dear Galaxy users, I have installed a local Galaxy instance on a server and I use it to run certain genomic assembly workflows. Nevertheless with larger datasets completion may take up to one day. How can i make Galaxy to continue the operation even when i close the browser? Is that possible on a local instance or on the main server? Thank you, Efthymios Ladoukakis ___ 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/ ___ 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: tool restrict access
Ivan, #if $__user_email__ == displayYou are not authorized to use this tool/display #else command interpreter=python data_source.py $output $__app__.config.output_size_limit /command To make this approach work, the email check should go in the command tag. More information: If you're looking to require users to login before using any tools, you can use this flag in the universe config file: # Force everyone to log in (disable anonymous access). #require_login = False If you're looking to implement tool-based access control, the best approach is probably to use the same role-based approach that libraries use: https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-to-restrict-tool Thanks, J. ___ 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: tool restrict access
Ivan, tool name=UCSC Main id=ucsc_table_direct1 tool_type=data_source descriptiontable browser/description command interpreter=python #if $__user_email__ == displayYou are not authorized to use this tool/display #else data_source.py $output $__app__.config.output_size_limit #end if /command ... and I got the error below, which seems connected to the cheetah syntax. Any idea of what I'm doing wrong? As is tradition in python, you need to put semi-colons after conditionals. E.g. -- #if $__user_email__ == : displayYou are not authorized to use this tool/display #else: data_source.py $output $__app__.config.output_size_limit #end if -- J. ___ 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] User name / public name confusion.
Good catch Jeroen. It's fixed on the development branch in changeset 0d1d62b8be2e J. On Jan 11, 2012, at 9:04 AM, J. F. J. Laros wrote: Dear developers, Subject: Minor issue - Confusion about public / user name. Description: When creating an account or managing user information, the error ``User name must contain only lower-case letters, numbers and '-''' may occur if the user chooses an invalid public name. This error can be confusing when the user tries to search for a ``User name'' field. Perhaps this error should mention the field name. With kind regards, Jeroen. -- Jeroen F. J. Laros - j.f.j.la...@lumc.nl ___ 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: tool restrict access
May you suggest me how to sketch a simple python script that prints in the central section of the galaxy window a message like you are not authorized to execute this tool ? This isn't possible right now, hence my reference to the open Bitbucket issue regarding this limitation. The best you can do right now is (a) restrict tool access to non-anonymous users or (b) cause the tool not to run by manipulating the command line in the template and, by printing to stderr, cause Galaxy to report the job failed. Best, J.___ 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] An error occurred...
Milos, Can you share your history with me (Options - Share or Publish - share with a user -- my email address) and I'll take a look. Thanks, J. On Jan 16, 2012, at 12:46 PM, Milos Busarcevic wrote: Hi, I've got this message after trying to run Cufflinks on the Main instance: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Is this a global problem and is there a way to fix it? Thanks, Milos ___ 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] An error occurred...
Milos, I successfully ran Cufflinks on your datasets; I've shared the history with you that has the results. Perhaps you ran into a transient error. Best, J. On Jan 17, 2012, at 8:13 AM, Milos Busarcevic wrote: Hi Jeremy, I have shared my history with you. Today, error that appears when I try to run cufflinks has changed into: Error executing tool: 'hg19'. Thanks, Milos On Mon, Jan 16, 2012 at 7:21 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Milos, Can you share your history with me (Options - Share or Publish - share with a user -- my email address) and I'll take a look. Thanks, J. On Jan 16, 2012, at 12:46 PM, Milos Busarcevic wrote: Hi, I've got this message after trying to run Cufflinks on the Main instance: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Is this a global problem and is there a way to fix it? Thanks, Milos ___ 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] problems with location of filter bar in trackster
Hans, A couple questions: (a) What browser/OS are you using when seeing this problem? (b) Can you replicate this behavior on our public server? A couple notes: depending on your Web server setup, it may be necessary to use the packed Trackster script rather than the full one. Also, we're planning to release a new distribution in the next couple days, so it may be worthwhile to put off debugging Trackster until then because there have been quite a few changes to Trackster since the last release and these may solve your issues. Thanks, J. On Jan 18, 2012, at 9:19 AM, Hans-Rudolf Hotz wrote: Hi I am still in the process of upgrading all our Galaxy servers to the current changeset (b258de1e6cea, Nov. 18) and now I am running into troubles with the visualization: Depending on the location of my mouse, the filter bar and the other extra buttons jump between two positions, which makes it impossible to use, see Screenshot_1.png and Screenshot_2.png I was looking for relevant code changes, which were committed after Nov. 18. I found changeset 856aac70b018 (Trackster: refactor action icon creation and initialization from Nov. 23) for ~/static/scripts/trackster.js Adding this change fixes the problem somehow, but I lose the original icons (for 'set display mode', 'Hide/Show track content', etc) and the bar is now below the track, see Screenshot_3.png Just using the ~/static/scripts/trackster.js from 'central' doesn't solve the problem either. Are there any extra steps I can do in addition to changeset 856aac70b018 in order to solve this problem (except for waiting/using for the next release) Thank you very much for your help Hans Screenshot_1.pngScreenshot_2.pngScreenshot_3.png___ 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] problems with location of filter bar in trackster
it works fine on the public server Good, this narrows down the problem to installing the -central script on your instance b/c main's copy of the script is very similar to -central's. what do you mean by packed Trackster script All JavaScript files are compressed in size--comments/whitespace removed and variables renamed--to minimize their transfer time. These are available in /static/scripts/packed If you have directives in your proxy server config to use the packed scripts, you'll want to update the packed script from -central as well. The other thing to consider is browser caching: you may need to clear your browser cache to load the new Trackster script. Good luck, J. ___ 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] naming of history steps
Brad, But I think it might be a lot easier to manage if step names were based on the titles of the history items instead of data 2 or whatever. Has this been tried and rejected for some reason? It's been tried and rejected because dataset names get very long and unwieldy. E.g. Sam/Bam Alignment Summary Metrics on Tophat on Filter FASTQ on my_rna_seq_reads Would a pull request implementing this change be welcomed? What we imagine would help is a way to easily show/find a dataset's analysis path -- its parents and its decendants -- so that it's possible to trace the datasets/tools used to create a dataset and the tools/datasets subsequently used. This is something we'd like to do but haven't put much effort into yet. Community contributions in this space would be great. Best, J. ___ 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] naming of history steps
Ususally the most important information is the first and last step E.g. The TopHat run should be called TopHat on SOLiD 24A The alignment stats should be SAM/BAM Summary Metrics of Solid 24A With the rest of the tools in the chain identified in the more information box. This would also give graph generating tools a fighting chance to present something useful in any graphs generated. E.g. GC Bias Plot of Solid 24A could have a title of Solid 24A instead of dataset_234.dat What do you think of this first-last model? This model breaks down during experimentation. E.g. let's say three different methods for trimming a FastQ dataset are tried before mapping with Bowtie. Currently, the Bowtie runs are named differently b/c each trimmed dataset is a unique input. Using first-last model, all datasets are named the same and it is not possible to differentiate b/t them without looking at the inputs, which requires clicking on the rerun/info button and finding the input(s). The current approach used by Galaxy lists the inputs in the dataset title to avoid these issues. Datasets with the same name becomes more problematic as more steps are added b/t first and last because, while they have the same name, the steps taken to produce them may be very different. The first-last model could be nice for workflows, though, perhaps as an extension of the rename dataset actions or a kind of global rename dataset action. J. ___ 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] Feature requests - viewing data and annotations
Hi Shaun, Restricting datasets to show only the first megabyte is a great idea when dealing with large data files but sometimes I want to see the end of a file to check it is complete or to check the progress of a running job. At the moment I use the helper script to find the file on the server and then use tail. Would it be possible to add a button in the dataset view (next to show all and save) that allows you to see the end of the file? This is a good idea. Ideally I would like to have a large area to add notes while still being able to view datasets. Perhaps turning on annotation could split the main pane in to 2 areas with adjustable size with an annotation area on the bottom? Maybe there would be a way to link Galaxy pages directly to histories? I'm not sure what the best way to implement this would be but I'd like to see an improvement. A larger annotation area--with a fully-featured editor like that in Pages--is also a good idea. However, there are no immediate plans to implement either of these ideas in the near future. Community contributions are always welcome, though. Best, J. ___ 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] advanced parameters: all or nothing?
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu wrote: Hello, I was recently adjusting advanced parameters when running Tophat in Galaxy and noticed that when advanced parameters are used, every field is converted and submitted as command line parameter to the tool at runtime. Without changing any of the default values I get a different tophat result than if advanced parameters are left off. That sounds like a bug in the wrapper. Recent Tophat versions have changed parameters and default values again. I made the following changes in 3bd8bed55631 to make the wrapper compatible with Tophat 1.4.0: *removed junctions_filter parameter *changed the default value for max-mismatches from 40 to 20 This should ensure that enabling advanced parameters but leaving them untouched yields the same results as using default parameters. J. ___ 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] advanced parameters: all or nothing?
Wouldn't it be better not to have the default value 40 (or 20) in the wrapper at all? i.e. Leave it out, so that by default that argument isn't used, so that tophat uses the default it wants to use. This would work but limits reproducibility and transparency because Galaxy wouldn't have a record of the parameter's actual value. Yes, this is a problem when default parameters are used as well and should be fixed. However, making more use of defaults when advanced setting are used could be especially problematic b/c I imagine that using advanced parameters generally implies that a user cares are default values more so than if using all defaults. FWIW, the Galaxy team has started thinking about how to better handle multiple tool versions and different parameter default values for different tool versions. If anyone has strong feelings, please feel free to start a discussion (in a new thread please) on this challenge. Best, J. ___ 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] generate dynamic select list based on other input dataset
Holger, Have you looked at how dynamic options work and whether they would be sufficient for your use? See thefilter tag syntax for details: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set To specifically address your problem: can you determine the particular place where the syntax error is appearing? And can you provide a link to the thread that you're using as a starting point? Thanks, J. On Feb 10, 2012, at 3:43 PM, Holger Klein wrote: Dear all, I'm still stuck with the problem to dynamically generate an option list extracted from a user-selectable input dataset. Does anybody have experience here, or is this not possible at all? Have a nice weekend, Holger On 02/07/2012 09:58 PM, Holger Klein wrote: Dear all, I have a working module which generates wig files for genomic annotation from a single column of a bigger input data matrix (Input A). In the current state, the user has to input the column name (Input B) from which to calculate the values in the wig file. Now I'd like to modify the xml in such a way, that depending on the input dataset (Input A) a dynamic list for Input B is generated. I found Hans-Rudolf Hotz' hints from some time ago on this list and thought that the following would be a good start: param name = InputB label = InputBName format = data type = select help = Use tickboxes to select model display = radio dynamic_options = getInputBOptions($InputA) / code file=getInputBOptionsFromInputA.py getInputBOptionsFromInputA.py contains a single function def getInputBOptions($InputA): ## parse Input A ## create list InputBOptions return(InputBOptions) Using this approach I get an invalid syntax message when trying to even open the module - in any case I have the feeling that something is still missing here. Did anybody solve a similar problem already and could give me a hint on how to solve that? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511 ___ 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 executing tool: 'hg19'
Hello Joachim, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work. What are the steps you're taking to produce this issue? They all send this error message: Error executing tool: 'hg19' Are you seeing this error in failed datasets? If not, where are you seeing this error? This bug has been reported before, but I was wondering if somebody suggest a fix for this? Can you provide a link to the thread/issue where this has been reported? Thanks, J. ___ 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 executing tool: 'hg19'
This bug has been fixed in galaxy-central but, as per one of the threads you found, has not made it to galaxy-dist yet. Try this: 1. assuming you haven't made any changes to datatypes_conf.xml, copy datatypes_conf.xml.sample to datatypes_conf.xml 2. visit the custom builds page (User tab -- Custom Builds) and see if the Page loads properly; if it does, your custom build should work and everything should be fine. 3. this is a user-specific problem, so you can always create a new user and you should be good to go. If you want to continue to use the problematic account and the above doesn't work, you'll need to manually--via SQL--delete the user preferences for the problematic user. Best, J. On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote: For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release'). Hello Joachim, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work. What are the steps you're taking to produce this issue? I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the dataset . In the next screen: save in new visualation, which I called test. And I selected there 'Add a custom build'. Next I could select which fasta from my history containing the reference: selected the correct one. I named it hg19_chrom21. But then, clicking OK, gave an error. From then on, all tools give the error: Error executing tool: 'hg19'. The point is, I cannot recreate that BAM file, since the required tools are not working anymore... Basically, my Galaxy has become useless. Before I dig up my backup, I hope somebody can help me? They all send this error message: Error executing tool: 'hg19' Are you seeing this error in failed datasets? If not, where are you seeing this error? This error appears in the middle pane, after clicking execute. This bug has been reported before, but I was wondering if somebody suggest a fix for this? Can you provide a link to the thread/issue where this has been reported? http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html Thanks, J. Thank for looking into this. ___ 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 executing tool: 'hg19'
Can you confirm that the following lines are in your datatypes_conf.xml file? -- datatype extension=fasta type=galaxy.datatypes.sequence:Fasta display_in_upload=true converter file=fasta_to_tabular_converter.xml target_datatype=tabular/ converter file=fasta_to_bowtie_base_index_converter.xml target_datatype=bowtie_base_index/ converter file=fasta_to_bowtie_color_index_converter.xml target_datatype=bowtie_color_index/ converter file=fasta_to_2bit.xml target_datatype=twobit/ converter file=fasta_to_len.xml target_datatype=len/ /datatype -- If so, the other issue is that you'll need to restart Galaxy in order for the changes to take hold. Apologies for not mentioning this step previously. J. On Feb 14, 2012, at 3:18 AM, Joachim Jacob wrote: First, thanks. I just created a new user, and I am ready to go with that user. FYI, the reset of the datatypes_conf.xml did not do the trick: following error appears on the custom builds page: NoConverterException: Conversion from 'fasta' to 'len' not possible Thanks, Joachim On 02/13/2012 06:02 PM, Jeremy Goecks wrote: This bug has been fixed in galaxy-central but, as per one of the threads you found, has not made it to galaxy-dist yet. Try this: 1. assuming you haven't made any changes to datatypes_conf.xml, copy datatypes_conf.xml.sample to datatypes_conf.xml 2. visit the custom builds page (User tab -- Custom Builds) and see if the Page loads properly; if it does, your custom build should work and everything should be fine. 3. this is a user-specific problem, so you can always create a new user and you should be good to go. If you want to continue to use the problematic account and the above doesn't work, you'll need to manually--via SQL--delete the user preferences for the problematic user. Best, J. On Feb 13, 2012, at 10:30 AM, Joachim Jacob wrote: For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release'). Hello Joachim, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work. What are the steps you're taking to produce this issue? I had a BAM file that I wanted to test to view with Trackster. I clicked that icon in the dataset . In the next screen: save in new visualation, which I called test. And I selected there 'Add a custom build'. Next I could select which fasta from my history containing the reference: selected the correct one. I named it hg19_chrom21. But then, clicking OK, gave an error. From then on, all tools give the error: Error executing tool: 'hg19'. The point is, I cannot recreate that BAM file, since the required tools are not working anymore... Basically, my Galaxy has become useless. Before I dig up my backup, I hope somebody can help me? They all send this error message: Error executing tool: 'hg19' Are you seeing this error in failed datasets? If not, where are you seeing this error? This error appears in the middle pane, after clicking execute. This bug has been reported before, but I was wondering if somebody suggest a fix for this? Can you provide a link to the thread/issue where this has been reported? http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg04216.html http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg03995.html Thanks, J. Thank for looking into this. ___ 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] advanced parameters: all or nothing?
So is the behavior of the optional=true tag that if the field form is left empty for that parameter then it will not be passed to the tool? Optional is enforced at the UI level; a wrapper can choose to handle optional parameters differently. I am wondering if a more sophisticated behavior on the UI side of things for the optional tag would still allow for recording that the parameter is using the default value for the version of that tool but not actually pass that parameter on the command line in case it influences the behavior of the tool? Thinking of parameters that should have a default value but whose actual presence on the command line changes what happens. Though, I guess this could be done by simply deleting the default value in the optional parameter has one? Maybe if the optional tag enabled the parameter itself to be toggled on/off (grayed out/regular text)? This way a block of advanced parameters could be enabled without requiring that they all be passed to the tool (or deleting all their values if they are marked optional). There are two issues to consider: (1) Whether the UI is friendly when a tool has many parameters. Clearly, there are improvements to be made, but Galaxy makes it relatively easy to ignore parameters that aren't of interest. A novel UI approach might try to make it easier to hide unwanted parameters from view or selectively set certain parameters. (2) Whether optional parameters should be passed to the wrapper. IMHO, there's no reason not to make all user input available to the wrapper. A tool that doesn't produce the same output when (a) parameter values are not specified and (b) default parameter values are specified is buggy and should be fixed. Best, J. ___ 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] Trackster traceback on C. Cerevisiae mapped data
Alex,
Generally cPickle errors when loading summary trees are a result of indexing
gone bad.
Here are a couple notes that should save you some work:
*your bowtie indices and 2bit files do not need to be rebuilt; they are not
generating these errors;
*converting your SAM files to BAM may provide a short-term solution; Trackster
SAM support is new and not well tested yet.
Finally, there are many Trackster fixes in galaxy-central, and I believe some
of them may solve your issues. For SAM datasets, your best bet is to either (a)
try visualizing the datasets with -central or (b) wait for the upcoming
(planned for next week) -dist update. If you're still getting errors with the
new code base, let us know.
Thanks,
J.
I'm running the latest galaxy-dist and Trackster appears to be generally
working since I added a couple of reference genomes and users were able to
visualize their data. I just rebuilt all relevant references for the sacCer3
(dbkey) genome by concatenating the UCSC chromosome fasta files and building
both 2bit file and the bowtie index from the resulting fasta file. The
reference genome comes up in the Trackster as I can see the sequence.
However, adding a track from the bowtie-mapped data freezes at the building
index stage and selecting a chromosome in Trackster produces an immediate
traceback. Logs are below.
Thanks,
Alex
10.25.137.177 - - [01/Mar/2012:12:56:50 -0400] GET
/tracks/converted_datasets_state?hda_ldda=hdadataset_id=0f5bae0d7db33d73chrom=chrIII
HTTP/1.1 500 -
http://galaxy.hpc.ufl.edu/tracks/browser?dataset_id=0f5bae0d7db33d73id=9b03f356ffec3bf6;
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_3) AppleWebKit/535.11 (KHTML,
like Gecko) Chrome/17.0.963.56 Safari/535.11Error - type
'exceptions.EOFError':URL:
http://galaxy.hpc.ufl.edu/tracks/converted_datasets_state?hda_ldda=hdadataset_id=0f5bae0d7db33d73chrom=chrIIIFile
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__ app_iter = self.application(environ,
start_response)File
'/galaxy/run/prod/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in
__call__ return self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/middleware/remoteuser.py', line
111 in __call__ return self.app( environ, start_response )File
'/galaxy/run/prod/eggs/Pas!
te!
-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return
self.application(environ, start_response)File
'/galaxy/run/prod/lib/galaxy/web/framework/base.py', line 160 in __call__
body = method( trans, **kwargs )File
'/galaxy/run/prod/lib/galaxy/web/framework/__init__.py', line 67 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ) )File
'/galaxy/run/prod/lib/galaxy/web/controllers/tracks.py', line 546 in
converted_datasets_state if not indexer.has_data( chrom ):File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/data_providers.py', line
566 in has_data st = summary_tree_from_file(
self.converted_dataset.file_name )File
'/galaxy/run/prod/lib/galaxy/visualization/tracks/summary.py', line 92 in
summary_tree_from_file return cPickle.load(open(filename, rb))EOFError:
CGI Variables
-
QUERY_STRING: 'hda_ldda=hdadataset_id=0f5bae0d7db33d73chrom=chrIII'
WSGI Variables
--
application: paste.recursive.RecursiveMiddleware object at 0x6323cd0
paste.cookies: (SimpleCookie:
__utma='239163719.1605318534.1329425338.1330006360.1330438487.6'
__utmc='239163719'
__utmz='239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided)'
auth_probe='1'
auth_tkt='ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D'
galaxysession='86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe',
'galaxysession=86cf583f63ab6865e8a46aa482c17c1f6ea618d0f448986bf2fc440587db06af6b9d9ac4eccca0fe;
auth_probe=1;
__utma=239163719.1605318534.1329425338.1330006360.1330438487.6;
__utmc=239163719;
__utmz=239163719.1329425338.1.1.utmcsr=google|utmccn=(organic)|utmcmd=organic|utmctr=(not%20provided);
auth_tkt=ZWE0ZmY3MjkxYjdhM2Y0NWRkMjVhNTVkZWUzODBhYzc0ZjRmODRlYm9tQGhwYy51ZmwuZWR1ITEwMDAsMTAwMyFtYWxleDpPbGVrc2FuZHIgTW9za2FsZW5rbw%3D%3D')
paste.expected_exceptions: [class 'paste.httpexceptions.HTTPException']
paste.httpexceptions: paste.httpexceptions.HTTPExceptionHandler object at
0x631c890
paste.httpserver.thread_pool: paste.httpserver.ThreadPool object at
0x1314b10
paste.parsed_querystring: ([('hda_ldda', 'hda'), ('dataset_id',
'0f5bae0d7db33d73'), ('chrom', 'chrIII')],
'hda_ldda=hdadataset_id=0f5bae0d7db33d73chrom=chrIII')
paste.recursive.forward: paste.recursive.Forwarder from /
paste.recursive.include: paste.recursive.Includer from /
paste.recursive.include_app_iter: paste.recursive.IncluderAppIter from
Re: [galaxy-dev] Trackster cannot display INTERVAL or GATK-INTERVAL files???
Thon, It seems that trackster does not know how to display INTERVAL files? Is that true? Yes, this is currently a limitation. However, most of the work is done that is necessary to make this happen, so it should be done soon, definitely in the next month or two. Surely there is an easy way to support those kinds of simple files without having to convert them? As you discovered, conversions can be done by clicking on the pencil icon and then performing the conversion. We're aware that isn't ideal for usability and plan to improve it in the future. J. ___ 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] refresh_on_change is broken?
Leandro, refresh_on_change is used quite a bit throughout the tool UI and appears to work fine both on a local instance and on the public instance. E.g. look at Tophat and change settings from 'Use Defaults' to 'Full Parameter List' -- the refresh_on_change works on reload the tool with more parameters. Some questions that should shed light on your issues: *Does the Tophat tool refresh on the main server? If not, this is probably a browser issue. *Are you seeing any errors in the Javascript console? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools? Thanks, J. On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote: Hi everyone, Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to, no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished? sincerely, Leandro On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hello, Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem? regards, Leandro ___ 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] refresh_on_change is broken?
Maybe we don't understand the feature in the documentation, but this isn't the refresh_on_change functionality. In the Tophat tool XML there are no refresh_on_change=true attributes, you are talking about a conditional tag which when changing will refresh the page in order to expose different parts of a form depending on then value chosen, this is a different use case. The conditional tag has refresh_on_change added automatically and is used by Javascript accordingly. The feature we thought exists from the wiki docs is a utility refresh_on_change=true attribute that you can put on any input param tag which will cause the page to refresh with the changed state when you change the param. It's supposed to replace the deprecated pages tags. Unless there is undocumented functionality, refresh_on_change cannot be explicitly used: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Once we started needing to make more complex form logic you realize that this is not just very useful but necessary. Here's one example: inputs param type=data name=dataset refresh_on_change=true label=Select a file from you history / param type=select multiple=true name=dataset_values dynamic_options=get_options_from_file(dataset.file_name) / /inputs If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively. Page should refresh automatically when dataset is changed and dynamic options are used. If not, it's a bug. J. Does this feature I describe to replace the deprecated pages tags not exist or just isn't fully implemented yet? regards, Leandro Some questions that should shed light on your issues: *Does the Tophat tool refresh on the main server? If not, this is probably a browser issue. *Are you seeing any errors in the Javascript console? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools? Thanks, J. On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote: Hi everyone, Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to, no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished? sincerely, Leandro On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hello, Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem? regards, Leandro ___ 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] potential bug in DefaultToolAction collecting chrom info
Andrew, You are correct. I've made this change in galaxy-central changeset 4d48285fcaa6 Thanks, J. On Mar 20, 2012, at 9:18 PM, Andrew Warren wrote: Hello, In the file lib/galaxy/tools/actions/__init__.py for the execute function of the DefaultToolAction class line 198 has the following code: if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): In this case trans.user.preferences[ 'dbkeys' ] is just returning a json string version of the dictionary. The result is that if input_dbkey is a substring of any part of this then it will be returned as True. Something like this would fix (though with the next lines of code it would be converting from json twice): if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in from_json_string(trans.user.preferences[ 'dbkeys' ] )): Cheers, Andrew ___ 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] refresh_on_change is broken?
A final pointer: to see tools that use dynamic options, take a look at Extract GFF features and Filter GFF dataset by feature count Good luck, J. On Mar 22, 2012, at 12:15 PM, Greg Von Kuster wrote: It's always best to look at examples in the code base for technical details like this rather than the wiki. You probably will need a combination of a conditional constructor along with a select list item in your tooll There are many tools that include these types of constructors that refresh the page when a when condition is met. One example is the extract_genomic_dna.xml tool config, which includes the following tag sets. inputs param format=interval,gff name=input type=data label=Fetch sequences for intervals in/ param name=interpret_features type=select label=Interpret features when possible help=Only meaningful for GFF, GTF datasets. option value=yesYes/option option value=noNo/option /param conditional name=seq_source param name=index_source type=select label=Source for Genomic Data option value=cachedLocally cached/option option value=historyHistory/option /param when value=cached /when when value=history param name=ref_file type=data format=fasta label=Using reference file / /when /conditional param name=out_format type=select label=Output data type option value=fastaFASTA/option option value=intervalInterval/option /param /inputs Sorry, but I don't have the time to get too much more involved in this than I have - as always, I'm stretched as thin as can be. Good luck! On Mar 22, 2012, at 5:09 AM, Leandro Hermida wrote: Dear Greg, On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster g...@bx.psu.edu wrote: Leandro, For refresh_on_change to work you need a set of optional selections and a set of refresh_on_change values, so in your example, the type should probably be a select instead of data. You'll also need the select list options to be generated based on your history items (at least that's what I think you're attempt here), so your list of refresh_on_change values will be attributes of those history items. Greg Von Kuster Could you show an example of this functionality that you described? This is new to me I really apologize and I looked for things on the Galaxy wiki but couldn't find. How would one do the simple example I illustrated in this thread: inputs param type=data format=txt name=dataset label=Select a text file from you history / param type=select multiple=true name=dataset_values dynamic_options=get_options_from_file(dataset.file_name) / /inputs Where in the tool form if the user changes the first drop-down menu to select a different file of a particular format from their history it will cause a refresh of the page so that the dynamic_options function in the second menu can be re-executed using the new file name as a parameter then generating new options in this second menu? regards, Leandro On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote: Here's one example: inputs param type=data name=dataset refresh_on_change=true label=Select a file from you history / param type=select multiple=true name=dataset_values dynamic_options=get_options_from_file(dataset.file_name) / /inputs If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively. Page should refresh automatically when dataset is changed and dynamic options are used. If not, it's a bug. Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work? regards, Leandro ___ 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] Formatting has lost the horizontal rule dividers in new Galaxy style
Greg, 1. The horizontal rule dividers specified by a - in the text have disappeared. Fixed in galaxy-central changeset cb5ff5b1bd67 2. Also I spotted a change where this .. - line 1 of some bullets - line 2 of some bullets Following line. .. lost the blank line after the line 2 line. Where exactly is this occurring? Thanks for the feedback, J. ___ 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] Cufflinks inconsistency ...
Kory, Cufflinks quantifies transcripts in parallel, and the inconsistencies that you're seeing are likely the result of these processes finishing in different order during different runs. To address this issue, you can use the Galaxy sort tool. Ultimately, this is not a Galaxy issue but an issue with the Cufflinks tool. You could drop the Cufflinks authors a note if you feel strongly about this inconsistency: tophat.cuffli...@gmail.com Finally, please use the galaxy-user mailing list for questions about tool usage. The galaxy-dev list is for local installation and tool development questions. Best, J. On Mar 21, 2012, at 10:51 AM, Johnson, Kory (NIH/NINDS) [C] wrote: Hello, I performed 6 different runs of Cufflinks using the same Reference Annotation on 6 different samples. I expected the resulting tabular output to be constant given the same Reference Annotation was used each time. What I found is that there was an inconsistency. Specific example, here is top 5 rows from output for one of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_idlocus length coverage FPKMFPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0OK NM_001005221 - - NM_001005221 - - chr1:367658-368597- - 0 0 0OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0OK Here are top 5 rows from output for another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_idlocus length coverage FPKMFPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0OK NM_001005221 - - NM_001005221 - - chr1:367658-368597- - 0 0 0OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 15114.7 9501.2120728.1 OK Here are top 5 rows from output for yet another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_idlocus length coverage FPKMFPKM_conf_lo FPKM_conf_hi FPKM_status NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0OK NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0OK NM_001005221 - - NM_001005221 - - chr1:367658-368597- - 0 0 0OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 28376.8 20008.936744.6 OK As a user, when selecting the same Reference Annotation to be used. I would expect the index of results by tracking id to be the same. Why is this happening? Why are they not consistent? If were to concat the above results across samples without correcting the indices, my data would be all
Re: [galaxy-dev] Create and Transfer Galaxy Page
Hi Todd, [Not sure if this is better suited to galaxy-dev or -user, so I'm sending to both]. galaxy-user is most appropriate for this question because it related to usage of Galaxy; galaxy-dev is for local installation and tool development questions. My question is - can I create a Galaxy 'Published Page' from my local Galaxy instance/histories, and then transfer that page to the main Galaxy instance? Not currently, though this is in our long-term plan. The reason is that I cannot make my local Galaxy instance public, as I am using a campus resource to host our galaxy. If this is possible, how can I do that? If not, any other ideas? It is possible to move datasets and workflows relatively easily between instances, so I'd recommend that: (a) you move your data and workflows to our public instance; (b) rerun your analyses on the public instance to create the required; (c) create and host the Page on our public instance. You can be assured that we will maintain our public server over the coming years and your Page will remain available and have a stable URL. Also, are there any tutorials/pages on how to create Published Pages in Galaxy in the first place? Not yet, though the idea is for the Page editor to be self explanatory. Here's how to get started with Pages: (a) from User menu, go to Saved Pages; (b) create a Page; (c) edit the Page using the Web-based editor; there are menus for inserting embedded datasets, workflows, histories, and visualizations as well as performing standard word-processing operations. Let us know if you have problems/questions and we'll start a guide for creating Pages. Best, J. ___ 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] Potential database corruption with local galaxy instance
Simon, Error executing tool: (ProgrammingError) column params of relation job does not exist This is your problem. This column should have been created in migration script 93, but for some reason it wasn't. The first step is to determine if subsequent migration scripts failed as well. Run this query against your Galaxy database: SELECT * FROM migrate_version; What is the version? Also, for completeness, what database are you using? Something else you can try is downgrading your database revision and then upgrading to see if you can find the problem. From a command line in your galaxy directory, do this: % sh manage_db.sh downgrade 92 % sh manage_db.sh upgrade You may want to back up your database before trying anything to ensure that you can rollback if something goes wrong. J. ___ 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] How to specify RUM output dir?
I’m good with everything except the output dir. I can’t figure out how to pass that directory information from Galaxy to the RUM_runner.pl in such a way that Galaxy will be able to subsequently capture the data. Does anybody have any advice, or can someone point me towards an existing wrapper that does something similar? You have two options: (a) you can set up the tool to report only a subset of outputs from the tool; or (b) you can use a composite datatype to store the complete directory: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Composite%20Datatypes Best, J.___ 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] Displaying genomic sequences in Trackster
Hi Naharajan, My best guess is that you've found some bugs. Fortunately, they are likely fixed in galaxy-central and will soon be available in galaxy-dist (we're planning an update in the next couple days). Once galaxy-dist is updated, please try updating your Galaxy instance and seeing if that fixes the problems. If not, let us know and we can take a closer look. J. On Apr 18, 2012, at 9:05 AM, Naharajan Lakshmanaperumal wrote: Dear all, We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine. We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done? 2) While saving the visualization, there is always an error message saying could not save visualization and it doesn't seem to be a web browser issue. How do we then save the visualization? Thanks in advance, Naharajan ___ 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] Potential database corruption with local galaxy instance
% sh manage_db.sh downgrade 92 % sh manage_db.sh upgrade The downgrade to 92 and upgrade created job.params. This is progress. You should be able to run jobs again, yes? Unfortunately, we are still getting errors about duplicate key values. The debug output when I try to export a history to a file is shown below my signature. Is there anything that was updated recently that would change primary keys? Primary keys are handled by SQLAlchemy, not Galaxy, so that's not the problem. I would guess the issue arose due to the missing 'params' column in job. This can likely be fixed by deleting all the rows in the job_history_export_table: DELETE FROM job_export_history_archive; The only downside to this operation is that existing history archives won't be found and will have to be recreated. Best, J. ___ 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] Default annotation track
Alex, It's not clear what the problem is. Trackster will handle an arbitrarily large number of contigs (albeit somewhat clumsily). What contig annotation data are you trying to preserve and/or provide access to? J. On Apr 19, 2012, at 11:30 AM, Oleksandr Moskalenko wrote: I needed to add a genome to the tracks in our local instance. However, the only available genome is a multi-fasta file of about 1800 supercontigs. I preserve the sanity of my clients I concatenated the fasta file and provided both versions. The unfortunate part is that the contig annotation data is lost in that conversion. I wonder if there is a way to extract the contig data as annotation and provide it as a default track in the concatenated genome or something like that. Any ideas? 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] How to specify RUM output dir?
yes: standard output: Broken pip yes: write error I know what this means, generally, but not in the context of Galaxy. Is this a telltale symptom, or is it too generic to say? Hard to say, but it's coming from your script and is indeed causing your job to fail. You might find it easier to debug if you run your tool/wrapper script from the command line. Best, J. ___ 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] linking Galaxy and Integrated Genome Browser
Hiral, I've cc'd the Galaxy development mailing list, which includes folks with experience in all areas of Galaxy. Can you be clear about what you're trying to do and what approach you're taking? Once it's clear what the issue is, someone can chime in with suggestions. Best, J. On Apr 19, 2012, at 12:44 PM, Hiral Vora wrote: Hi Jeremy, I have a question regarding committing my changes. I need to make changes to datatypes_conf.xml. But I see that repository does not have that file. So should I commit my changes to datatypes_conf.xml.sample instead? Thanks, Hiral ___ 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] putting up a SNP module on galaxy
Hi Xiangyu, This question is best directed to the galaxy development list, which I've cc'd. In general, to integrate a tool into Galaxy, you'll want to write a tool wrapper: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax and then upload it to the Galaxy toolshed: http://wiki.g2.bx.psu.edu/Tool%20Shed You can also upload workflows to the tool shed as well: http://wiki.g2.bx.psu.edu/Tool%20Shed#Enabling_workflow_sharing:_importing_a_workflow_via_a_URL Feel free to email the galaxy-dev list with any questions you may have. Best, J. On Apr 23, 2012, at 3:51 PM, Deng, Xiangyu (CDC/OID/NCEZID) (CTR) wrote: Hi Jeremy, My name is Xiangyu, working across street at the enteric disease laboratory branch, CDC. I built a SNP calling pipeline and want to put it somewhere with a friendly GUI so our/other wet lab persons can use it. I wonder if I can do it on Galaxy. The pipeline, written in python, uses bowtie 2, samtools, velvet, biopython and a perl program. Thanks, Xiangyu --- Xiang-yu Deng, Ph.D. ASM Fellow Enteric Diseases Laboratory Branch Division of Foodborne, Waterborne and Environmental Diseases National Center for Emerging and Zoonotic Infectious Diseases Centers for Disease Control and Prevention MS-C03, 1600 Clifton Road, Atlanta, GA 30333 Office: 404-639-1036 de...@cdc.gov ___ 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 on History export
Hi Todd, History export is a beta feature and hasn't been fully tested yet. We'll look into this, but it's difficult to diagnose a bug on a local instance. Can you reproduce on either our main or test server? Thanks, J. On Apr 25, 2012, at 8:08 PM, Todd Oakley wrote: Hello, I'd am trying to export histories to upload to another galaxy instance. For some histories, it works fine. However, for others, I get an error. When I turn on debug, I get the error pasted below. Any thoughts on what is the cause of object has no attribute 'hid'? Thanks! Todd Server Error Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ body = method( trans, **kwargs ) Module galaxy.web.controllers.history:591 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) Module galaxy.tools:1276 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) Module galaxy.tools.actions.history_imp_exp:103 in execute include_deleted=incoming[ 'include_deleted' ] ) Module galaxy.tools.imp_exp:419 in setup_job input_datasets = [ assoc.dataset.hid for assoc in job.input_datasets ] AttributeError: 'NoneType' object has no attribute 'hid' -- *** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *** ___ 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] New Tool - Can provide a template file to user
Either user can upload a spreadsheet for that or I shall provide a template file to fill up the data. When I checked there is no provision for uploading a speadsheet in my galaxy instance. Two simple options: (1) have users convert their spreadsheet data to csv/tabular format; Galaxy works well with tabular data. (2) create your own datatype: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes There are many examples for tabular data such as SAM, BED, GFF, etc., in the Galaxy base—see tabular.py and interval.py Best, J.___ 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] refresh_on_change is broken?
Let me give an example of something that I do. I have the user select a file after which I, using dynamic_options, extract the column names and present those to the user with a select input parameter. With the selected column name I then present a new select input parameter with all the unique values of the selected column. To get this to work I am now using three pages since it is really dynamic, thus after each parameter (that uses dynamic_options) I need to make a new page to use the selected item, thus: page param name=input_dataset type=data format=tabular, txt label=Input dataset / /page page param name=colfilter type=select multiple=False label=Select Filtering Column dynamic_options=get_columns( input_dataset ) / /page page param name=filter_values type=select multiple=True label=Select Filtering Values dynamic_options=get_filter( input_dataset, colfilter, 2 ) / /page This works fine, however it requires three pages which is deprecated. The documentation says 'use refresh_on_change' which is an undocumented feature (please (please!!) fix this!) with no examples anywhere on how to replace common page usage. refresh_on_change is not meant to be used explicitly in a tool's config file; it is an internal feature used by Galaxy to refresh pages as necessary, such as for conditionals. Also, dynamic_options has been deprecated in favor of the options tag. So given above example (which is similar to what the original requester asked), where to place the refresh_on_change option to get it working? If I'm reading your code right, this should be possible using the options tag only. First, select the dataset and then use something like for subsequent parameters: options from_dataset=input_dataset column name=name index=0/ column name=value index=0/ filter type=unique_value name=unique column=0/ /options Best, J. ___ 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 exporting history to file
Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote: Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error - type 'exceptions.TypeError': galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! 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/
