Re: [galaxy-dev] tool development
Hi Hans-Rudolf Yes, we have considered using data libraries, but for this particular use case we would prefer an approach like this. Our users are notoriously bad at data management and we would like to limit the amount of data that gets loaded in Galaxy. The networked share does not store all data permanently, so we need something to query what is available so the users can load that into their history. Ideally the datasets also shouldn’t be copied into Galaxy, but symlinked, if possible. Thanks for the tip on ‘dynamic_options’. Hadn’t noticed it before. Matthias > Op 19 jan. 2016, om 13:40 heeft Hans-Rudolf Hotz het volgende > geschreven: > > Hi Matthias > > Have you considered "Data Libraries"? > > A cron job can query your LIMS and use the API to create "Data Libraries". > Then the user can select which datasets she/he wants to import. > > > And back to your original question: Yes, it is possible to create interactive > tools. Check out the 'dynamic_options' examples on > > https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax > > > Regards, Hans-Rudolf > > On 01/19/2016 12:18 PM, Matthias De Smet wrote: >> Hi All, >> >> I would like to create a tool to import data from a sequencer on a networked >> share to a users history. >> The ideal setup would be that a query can be submitted to a database which >> contains all metadata from the sequencer + the path of the sequencer output. >> The tool should then show the available datasets found in the database and >> provide checkboxes to select which data should be imported. >> >> My question is: how do you guys propose I get started on this? Do I use the >> API? Is it even possible to get a tool to return some output without >> submitting it as a job, e.g. using it interactively? >> >> Thanks for the help! >> >> PS: I know the basics of tool development, but I haven’t got much >> experience, so all comments are welcome! >> >> Matthias >> ___ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] tool development
Hi Matthias Have you considered "Data Libraries"? A cron job can query your LIMS and use the API to create "Data Libraries". Then the user can select which datasets she/he wants to import. And back to your original question: Yes, it is possible to create interactive tools. Check out the 'dynamic_options' examples on https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Regards, Hans-Rudolf On 01/19/2016 12:18 PM, Matthias De Smet wrote: Hi All, I would like to create a tool to import data from a sequencer on a networked share to a users history. The ideal setup would be that a query can be submitted to a database which contains all metadata from the sequencer + the path of the sequencer output. The tool should then show the available datasets found in the database and provide checkboxes to select which data should be imported. My question is: how do you guys propose I get started on this? Do I use the API? Is it even possible to get a tool to return some output without submitting it as a job, e.g. using it interactively? Thanks for the help! PS: I know the basics of tool development, but I haven’t got much experience, so all comments are welcome! Matthias ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] tool development
Hi All, I would like to create a tool to import data from a sequencer on a networked share to a users history. The ideal setup would be that a query can be submitted to a database which contains all metadata from the sequencer + the path of the sequencer output. The tool should then show the available datasets found in the database and provide checkboxes to select which data should be imported. My question is: how do you guys propose I get started on this? Do I use the API? Is it even possible to get a tool to return some output without submitting it as a job, e.g. using it interactively? Thanks for the help! PS: I know the basics of tool development, but I haven’t got much experience, so all comments are welcome! Matthias ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.
I have created a Trello card to track this request here https://trello.com/c/qCtBBB8n. Any chance you can share the tool with me? I understand that this instinct is too simplistic - but it seems to me like the option to repeatedly run a tool over many datasets should not be the concern of the tool author - it is a user concern. If we add the option - perhaps we could stipulate that it requests some other parameter to dependent on it (I assume you have a dependent parameter in the repeat?). -John On Thu, Jan 22, 2015 at 5:50 AM, Vimalkumar Velayudhan wrote: > Thanks Peter. I see how this feature would be useful, but the program I'm > writing a wrapper for has an argument with values corresponding to the input > files. I am using a tag to maintain this order. With the multi-run > option, files are selected in a random manner and added to the job queue. It > is best not to display the multi-run option in this case. > > I see there is a TODO on this already: > https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084 > > For now, I have set allow=False but I believe this is best set at the param > tag level: > > > > > Vimal > > On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock > wrote: >> >> I think this is the (relatively new) Galaxy ability to automatically >> run N copies of your tool given N input files, making N outputs >> and is related to the collections work. >> >> (This is possible if your tool takes a single input file) >> >> Peter >> >> On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan >> wrote: >> > Hi all, >> > >> > I am trying to create a select box with the possibility of selecting >> > only a >> > single item from the input dataset (figure 1). This works fine but the >> > option for selecting multiple files is still visible (figure 2). The >> > multiple="false" attribute has no effect. >> > >> > Figure: http://i.imgur.com/oJVFCoF.png >> > >> > I have the following in my XML. >> > >> > > >label="Select Ribo-Seq alignment file" multiple="false" > >> > >> > >> > Any suggestions? >> > >> > galaxy-dist revision 5f4c13d622b8 >> > >> > >> > Regards, >> > Vimalkumar Velayudhan >> > >> > ___ >> > 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: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/mailinglists/ > > > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.
Thanks Peter. I see how this feature would be useful, but the program I'm writing a wrapper for has an argument with values corresponding to the input files. I am using a tag to maintain this order. With the multi-run option, files are selected in a random manner and added to the job queue. It is best not to display the multi-run option in this case. I see there is a TODO on this already: https://bitbucket.org/galaxy/galaxy-dist/src/a2308bdc93b897af974766b190abe019ade49e9a/lib/galaxy/tools/parameters/basic.py?at=default#cl-2084 For now, I have set allow=False but I believe this is best set at the param tag level: Vimal On Wed, Jan 21, 2015 at 2:26 AM, Peter Cock wrote: > I think this is the (relatively new) Galaxy ability to automatically > run N copies of your tool given N input files, making N outputs > and is related to the collections work. > > (This is possible if your tool takes a single input file) > > Peter > > On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan > wrote: > > Hi all, > > > > I am trying to create a select box with the possibility of selecting > only a > > single item from the input dataset (figure 1). This works fine but the > > option for selecting multiple files is still visible (figure 2). The > > multiple="false" attribute has no effect. > > > > Figure: http://i.imgur.com/oJVFCoF.png > > > > I have the following in my XML. > > > > >label="Select Ribo-Seq alignment file" multiple="false" > > > > > > > Any suggestions? > > > > galaxy-dist revision 5f4c13d622b8 > > > > > > Regards, > > Vimalkumar Velayudhan > > > > ___ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool development - Selecting a single item from input dataset.
I think this is the (relatively new) Galaxy ability to automatically run N copies of your tool given N input files, making N outputs and is related to the collections work. (This is possible if your tool takes a single input file) Peter On Tue, Jan 20, 2015 at 6:17 PM, Vimalkumar Velayudhan wrote: > Hi all, > > I am trying to create a select box with the possibility of selecting only a > single item from the input dataset (figure 1). This works fine but the > option for selecting multiple files is still visible (figure 2). The > multiple="false" attribute has no effect. > > Figure: http://i.imgur.com/oJVFCoF.png > > I have the following in my XML. > > label="Select Ribo-Seq alignment file" multiple="false" > > > > Any suggestions? > > galaxy-dist revision 5f4c13d622b8 > > > Regards, > Vimalkumar Velayudhan > > ___ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool development - Selecting a single item from input dataset.
Hi all, I am trying to create a select box with the possibility of selecting only a single item from the input dataset (figure 1). This works fine but the option for selecting multiple files is still visible (figure 2). The multiple="false" attribute has no effect. Figure: http://i.imgur.com/oJVFCoF.png I have the following in my XML. Any suggestions? galaxy-dist revision 5f4c13d622b8 Regards, Vimalkumar Velayudhan ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Development DELLY
Hi Marco, No problem - I originally copied the metadata access trick from one of the Galaxy dev-team's tool anyway. Maybe we need to add this to the wiki... Peter On Tuesday, January 13, 2015, Marco Albuquerque < marcoalbuquerque@gmail.com> wrote: > Hi Peter, > > I was unaware of how to access metadata, that seemed to be my issue. The > tool works now though! > > Thanks so much, > > Marco > > > > > On 2015-01-09 7:13 PM, "Peter Cock" > wrote: > > > >I think the symlink approach is best, see for example the Python > >wrapper script I used here for "samtools idxstats", > > > https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats > > > >However, you can make the link in the XML directly, see Dave's > >reworking of this wrapper: > > > https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection > >s/samtools/samtools_idxstats > > > >Regards, > > > >Peter > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Development DELLY
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque wrote: > Hello Galaxy, > > I'm currently working on adding some tools and am having an issue with > DELLY. > > So, I am under the impression that BAM indexing happens automatically when a > BAM is uploaded. However there is no associated dataset_i.dat.bai file in > the file location in my local instance of galaxy. > > There is however metadata which seems to be created but they are not being > linked together. What I mean to say is DELLY errors with cannot find Bam > Index. > > I was curious if there is a specific way developers are suppose to work > around this? Basically we want to avoid having to provide both the BAM and > BAM index and symbolically linking a new dataset because we know you have > already created a better implementation, we just want to use it and don't > know how. > > Any help is greatly appreciated, > > Marco I think the symlink approach is best, see for example the Python wrapper script I used here for "samtools idxstats", https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats However, you can make the link in the XML directly, see Dave's reworking of this wrapper: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats Regards, Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool Development DELLY
Hello Galaxy, I'm currently working on adding some tools and am having an issue with DELLY. So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy. There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index. I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how. Any help is greatly appreciated, Marco ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
