[galaxy-dev] Plotting tools - best output format? PDF, PNG, ...
Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the eye button acts like a download link. Is this a bug? If I switch to making a PNG file, then clicking on the eye button shows the image directly in the center panel (nice), but PNG is not a great format for detailed figures or printing. Looking over the tools which come with Galaxy under tools/plotting/*.xml all use PDF or PNG. How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? 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] Plotting tools - best output format? PDF, PNG, ...
On Wed, Apr 20, 2011 at 10:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the eye button acts like a download link. Is this a bug? Looks like a Firefox issue/setting - false alarm: On our local Galaxy, with a PDF entry in the history, and as a control http://nar.oxfordjournals.org/content/39/7/2492.full.pdf+html which should show a PDF embedded on the left: Windows XP, Internet Explorer 7.05730.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Chrome 10.0.648.204 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Firefox 3.6.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Linux CentOS, Firefox 3.6.13 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Firefox 4.0 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Safari 5.0.5 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. So it looks like Firefox can (probably dependent on the user's settings) download PDF files rather than show them in situ. That's fine, and not specific to Galaxy. 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, Great, I'm glad the workflow api is now working for you. I'm not sure what you mean with regards to work I'm doing for decrypting hda to actual id, but I will say that a History/Dataset API is something many people have asked about and I imagine that it will get done sooner rather than later, though I can't specify an exact timeframe. -Dannon On Apr 20, 2011, at 11:29 AM, t.yamagu...@utoronto.ca wrote: Hello Dannon, Thanks for the quick response. I emailed you as it seems to take some time to get authorization to reply to posts. I went though example_watch_folder.py and found the answer to resolve my problem. I thought the ids that returned from library_upload_from_import_dir.py were ldda but it was ld. Thanks. I have another question. I would like to access output files from each history using my script. I saw your previous posts and you're working on API to decrypt hda to its actual id. Are you planning to release the script in the near future? Thank you, Taka 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/ « [hide part of quote] ___ 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] Plotting tools - best output format? PDF, PNG, ... SVG!
On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all, ...cut... How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions. I looked at SVG about a year ago, and was pretty impressed. I did run into some issues, particularly with links, and opted to use PNG files in the end. Since then we've finally dropped IE6, so hopefully SVG would be safe now. Are your changes to add SVG as a datatype to Galaxy public? I'd like to suggest that be merged to the trunk. The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution). The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :( Do they cope with PDF? 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/
[galaxy-dev] Sample Tracking: How datasets are transferred from Sequencer to Galaxy
Hello, I was hoping someone could explain the process of how a dataset is transfered from a configured Sequencer to a Galaxy library within sample tracking. Particularly how RabbitMQ, API keys, transfer_manager_port and enable_sequencer_communication (in universe_wsgi.ini file) work in this process. Your help is greatly appreciated! Thanks Joe A. Cruz ___ 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] galaxy after logout
hi, In galaxy after logout by using browser back buttons i can able to go my home page .How to disable this facility can any one help -- Thanks Regards, Hari Krishna .M ___ 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/
