Re: [galaxy-dev] XML wrapper : use cheetath variable in from_work_dir tag

to be important to have them there Regards, Thon [cid:enz_logo_2_new36d101] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeb...@enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any

Re: [galaxy-dev] Is there a way yet to more easily determine name of inputs for renaming in workflows

the workflow editor accomplish what you need? -- James Taylor On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer tdeb...@enzymatics.commailto:tdeb...@enzymatics.com wrote: Hi, In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we

[galaxy-dev] Is there a way yet to more easily determine name of inputs for renaming in workflows

of workflow a tedious task... Regards, Thon [cid:enz_logo_2_new0600d5] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeb...@enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments

[galaxy-dev] Is there a way yet to more easily determine name of inputs for renaming in workflows

of workflow a tedious task... Regards, Thon [cid:enz_logo_2_newf03327] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeb...@enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments

[galaxy-dev] How to speed up submissions of workflows

Hi, I am routinely running hundreds of pair-end sequencing runs and find that STARTING a workflow on all of these can easily take hours since it seems each workflow preparation takes about 3 minutes, so for doing 128 fastq pairs like this it will take over 3 hours just to get all workflows

[galaxy-dev] When will the API allow setting of parameters (not inputs) from the API

Hi, One of the biggest hurdles for the implementation in our institute is the inability of Galaxy API to set parameters at run time. You can only seem to set inputs, but not parameters... Is there any ETA on when this will be available? Is this even a priority? Thanks! Regards, Thon de Boer,

Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

But this only works if you have a single dataset (such as a BAM file) for each workflow to run on. If you have pairs of files (such as paired end FASTQ files, not an uncommon workflow nowadays :) ) you need to resort to using the API, since there is no support for paired end sequencing in

[galaxy-dev] History items get REMOVED when using the API to run workflows

Hi, I am continueing to struggle with the API I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api). When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

Is this conference open for anyone or just (self appointed?) Czars? :) Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote: Also hello to everyone, As I browsed through those tabs which

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Jul 5, 2012, at 2:12 PM, Thon Deboer wrote: Hi, I am continueing to struggle with the API I have created a workflow execution engine that submits a workflow using the examples

Re: [galaxy-dev] Script not working in Galaxy

Check the Paster.log file...You probably will see an error there when it tries to load your file and it will be a clue how to fix it... Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Jun 21, 2012, at 5:55 PM, Ciara Ledero wrote: Hi

[galaxy-dev] Extracting the metrics files from a composite file such as Picard

Hi, Is there a way to extract the individual files from a composite file, such as the HTML files created by the picard tools? I would like to take the metrics files and use them further down in some workflow, but I only get an HTML file... While these HTML files are nice for quickly looking at

[galaxy-dev] links to datafile don't work in Postgres database?

Hi, I had no problems with providing my galaxy installation with datasets that were links to files in my filesystem, when I was using the SQLite database. But when I switched to a Postgres database, the links result in empty files when I choose links in the dataset upload. When I use actual

[galaxy-dev] Is there a way to pass key =value pairs to the output files in a programmatic way? (Tags? Metadata?)

Hi, I am trying to pass some key-value pairs to the result of a tool (such as the original sample name) but I cannot find a way to do this in the galaxy XML tool definitions. I am simply trying to retain in all the data files I produce, the name of the original sample which the results are

Re: [galaxy-dev] Is there a way to pass key =value pairs to the output files in a programmatic way? (Tags? Metadata?)

. Bioinformatics Guru LinkedIn Profile On Dec 31, 2011, at 2:26 PM, Thon deBoer wrote: Hi, I am trying to pass some key-value pairs to the result of a tool (such as the original sample name) but I cannot find a way to do this in the galaxy XML tool definitions. I am simply trying

Re: [galaxy-dev] Is there a way to pass key =value pairs to the output files in a programmatic way? (Tags? Metadata?)

be a way to rename an output file to the original input file in the workflow step Rename Dataset? Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Dec 31, 2011, at 4:17 PM, Peter Cock wrote: On Sat, Dec 31, 2011 at 11:43 PM, Thon deBoer