Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message
Hi Greg, Regarding the tools contained in fml_gff_converter_programs.tar.bz2, the following xml files are not well formed due to the malformed ! -- TODO EDIT HERE tag: fml_gff_converter_programs/galaxy/bed_to_gff3.xml fml_gff_converter_programs/galaxy/gff3_to_bed.xml fml_gff_converter_programs/galaxy/gff3_to_gtf.xml fml_gff_converter_programs/galaxy/gtf_to_gff3.xml In addition, none of these files include the required version attribute in the tool tag. Many thanks for pointing me the version number issue with tool configuration file. I forgot the same. The same goes for the files in ~/gff_groomer/fml_gff_groomer/galaxy - they are not well-formed due to the same ! -- TODO EDIT HERE tag, and they do not include the version attribute int the tool tag. Tools tags should look something like this: tool id=fml_bed2gff name=BED_to_GFF3 version=1.0.0 I've made some enhancements to the tool shed code that will display errors like this ( rather than resulting in the current server error ), so the next time I update the tool shed ( within the next couple of days ), this problem will be corrected. In the meantime, if you make the above corrections, you should have no problems uploading your tools to the tool shed. Thanks very much for pointing out these issues, and for taking the time to contribute your tools to the Galaxy community. Yes I did the changes accordingly and now it uploaded into the Tool shed. Thanks for your quick fix. regards, Vipin ___ 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] Setting min/max limit on repeat tag in tool XML file
Hi all, I'm working on a tool where the repeat tag looks like an elegant solution - however I want to limit the number of repeats to be 1, 2 or 3. i.e. I want to set min=1 and max=3 attributes for the repeat, based on analogy to the param tag. Is this possible, but not documented here? https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax In terms of the GUI, I'd like the page to preload with as many entries as the min setting (zero by default), and disable the add button once the max setting is reach (default no limit). (Alternatively you could validate the max/min when the form is submitted by clicking the execute button, but that seems less user friendly.) If this isn't already possible, would it be generally useful to add this? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Setting min/max limit on repeat tag in tool XML file
Hi Peter, Yes, setting min and max values in the repeat tag should work as you need. As you point out, it is probably not well documented, so please let us know if it isn't working as you imagine it should. Thanks for using Galaxy, Dan On Apr 19, 2011, at 6:47 AM, Peter Cock wrote: Hi all, I'm working on a tool where the repeat tag looks like an elegant solution - however I want to limit the number of repeats to be 1, 2 or 3. i.e. I want to set min=1 and max=3 attributes for the repeat, based on analogy to the param tag. Is this possible, but not documented here? https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax In terms of the GUI, I'd like the page to preload with as many entries as the min setting (zero by default), and disable the add button once the max setting is reach (default no limit). (Alternatively you could validate the max/min when the form is submitted by clicking the execute button, but that seems less user friendly.) If this isn't already possible, would it be generally useful to add this? Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Setting min/max limit on repeat tag in tool XML file
On Tue, Apr 19, 2011 at 1:46 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Peter, Yes, setting min and max values in the repeat tag should work as you need. As you point out, it is probably not well documented, so please let us know if it isn't working as you imagine it should. Thanks for using Galaxy, Dan Hi Dan, Excellent - that does pretty much what I was expecting. Thanks for updating the wiki page. It would be a nice refinement to hide the Remove buttons when at the minimum, and hide the Add button when at the maximum - but not essential. What I need to work out now is how to use repeat parameters in the unit tests. There seems to be examples in tools/mutation/visualize.xml and tools/plotting/xy_plot.xml which only use the first repeat... Also, can I access the repeat number for default values - e.g. I'd like to have a caption parameter defaulting to Set 1, Set 2 etc. Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] FTP upload of data
To be clear, you were able to connect to the galaxy server using WinSCP in plain FTP mode, and had no errors uploading the files? -Dannon On Apr 19, 2011, at 9:37 AM, vasu punj wrote: Dannon, I used winSCP to upload the files but dont see in Galaxy in history of uploaded files or even with URL? Any suggestion please. Thanks ___ 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] FTP upload of data
Ok, great. Please do remember to reply-all and include the list in the future. Among other things, it helps us immensely in keeping track of what has and has not been answered. -Dannon On Apr 19, 2011, at 9:43 AM, vasu punj wrote: I figured out and find files. Thanks. --- On Tue, 4/19/11, vasu punj pu...@yahoo.com wrote: From: vasu punj pu...@yahoo.com Subject: Re: [galaxy-dev] FTP upload of data To: Dannon Baker dannonba...@me.com Date: Tuesday, April 19, 2011, 8:37 AM Dannon, I used winSCP to upload the files but dont see in Galaxy in history of uploaded files or even with URL? Any suggestion please. Thanks --- On Mon, 4/18/11, Dannon Baker dannonba...@me.com wrote: From: Dannon Baker dannonba...@me.com Subject: Re: [galaxy-dev] FTP upload of data To: vasu punj pu...@yahoo.com Cc: galaxy-...@bx.psu.edu Date: Monday, April 18, 2011, 2:40 PM Vasu, No, a paid service is not at all required. jjw14's solution in that thread predates native FTP transfer to galaxy, and that sort of intermediate paid host is not necessary. Find detailed instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP -Dannon On Apr 18, 2011, at 3:32 PM, vasu punj wrote: Hi All, I was wondering if there are instructions for uploading data files (large) to Galaxy via FTP and if this is a paid service as per link : http://seqanswers.com/forums/showthread.php?t=5328 Thnaks. Vasu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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] Execution of workflows using API
Hello, I have a question regarding execution of workflows using API (workflow_execute.py). I am writing a script to automate file uploading and workflow execution using API. I was able to upload files and the response gave me ids for each file with 32 characters although the README example returned 16 characters. (I used library_upload_from_import_dir.py) Then I tried to execute a workflow using workflow_execute.py but it does not seem that the script accepts the ids. Is there any ways to resolve this issue? Thank you, Taka ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] BLAST+ HTML output broken
Hi Kanwei, I noticed that the BLAST+ output options for HTML are not working, a side effect of my recent refactoring. Could you transplant/merge this fix and test please: https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf https://bitbucket.org/peterjc/galaxy-central/changeset/c60551f7d13c These are the only commits on this new branch from the default: https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_04_19 Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Execution of workflows using API
Taka, Would you mind sharing the exact command you used to call workflow_execute.py? It does sound like you're doing something very similar to what scripts/api/example_watch_folder.py does. That script also uploads from the file system to a data library and subsequently executes a workflow on the uploaded files. If you haven't already taken a look there, it could perhaps serve as another example for you. -Dannon On 04/19/2011 10:51 AM, Takafumi Yamaguchi wrote: Hello, I have a question regarding execution of workflows using API (workflow_execute.py). I am writing a script to automate file uploading and workflow execution using API. I was able to upload files and the response gave me ids for each file with 32 characters although the README example returned 16 characters. (I used library_upload_from_import_dir.py) Then I tried to execute a workflow using workflow_execute.py but it does not seem that the script accepts the ids. Is there any ways to resolve this issue? Thank you, Taka ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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] bwa failure preparing job
Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.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] No Menu after submitting workflow
I'm getting inconsistent behavior when I run a workflow. I have one workflow,that when I run it, the green box indicating my workflow has been submitted shows up in the middle panel with Tools to the left, histories to the right, and menu above. For another workflow, I submit it successfully, but the green box ends up on a page with nothing but the green box. No tools, no history, no menus. Both of these are being done using the same browser session (running firefox on a mac). Thanks, Dave ___ 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] No Menu after submitting workflow
Dave, What revision of galaxy are you running (hg tip)? We've made a few changes quite recently to running workflows, though I haven't seen any errors like this yet. Also, what's different about the two workflows (history destinations, multiple-inputs, rename actions, etc.)? -Dannon On 04/19/2011 03:01 PM, Dave Walton wrote: I'm getting inconsistent behavior when I run a workflow. I have one workflow,that when I run it, the green box indicating my workflow has been submitted shows up in the middle panel with Tools to the left, histories to the right, and menu above. For another workflow, I submit it successfully, but the green box ends up on a page with nothing but the green box. No tools, no history, no menus. Both of these are being done using the same browser session (running firefox on a mac). Thanks, Dave ___ 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] No Menu after submitting workflow
ca0c4ad2bb39 is the last upstream change set in our fork (Glen is planning to update our fork with the latest dist later this week). Neither workflow does history destinations. Both histories have multiple inputs going to varying tools in the workflow. Both histories rename outputs. One workflow does tool hiding for modules that don't generate output (this is the one that behaved strangely in galaxy). The one that behaves strangely (doesn't have the message appear in the middle panel) is essentially the same workflow as the first, but with more steps, additional side paths, and quite a few more output files. When Glen updates to the latest dist, I'll try to reproduce the problem. Dave On 4/19/11 3:08 PM, Dannon Baker dannonba...@me.com wrote: Dave, What revision of galaxy are you running (hg tip)? We've made a few changes quite recently to running workflows, though I haven't seen any errors like this yet. Also, what's different about the two workflows (history destinations, multiple-inputs, rename actions, etc.)? -Dannon On 04/19/2011 03:01 PM, Dave Walton wrote: I'm getting inconsistent behavior when I run a workflow. I have one workflow,that when I run it, the green box indicating my workflow has been submitted shows up in the middle panel with Tools to the left, histories to the right, and menu above. For another workflow, I submit it successfully, but the green box ends up on a page with nothing but the green box. No tools, no history, no menus. Both of these are being done using the same browser session (running firefox on a mac). Thanks, Dave ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] BLAST+ HTML output broken
K On Tue, Apr 19, 2011 at 11:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Kanwei, I noticed that the BLAST+ output options for HTML are not working, a side effect of my recent refactoring. Could you transplant/merge this fix and test please: https://bitbucket.org/peterjc/galaxy-central/changeset/e1e6f92e07bf https://bitbucket.org/peterjc/galaxy-central/changeset/c60551f7d13c These are the only commits on this new branch from the default: https://bitbucket.org/peterjc/galaxy-central/src/blast_2011_04_19 Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
