Re: [galaxy-dev] Import files from local file system
On 21/02/2011 14:56, Nate Coraor wrote: Steve Taylor wrote: I think so. Just to double check is there a definitive way I can tell? In ./tools/data_source/upload.xml param name=ftp_files type=ftpfile label=Files uploaded via FTP/ So I got this to work by hacking basic.py. def visible( self ): self.tool.app.config.ftp_upload_dir = '/data/galaxy' self.tool.app.config.ftp_upload_site = 'localhost' I can now see my files in my user directory. What is the best part of the code to use log.warning() to see what's going on? How can tell if it is reading the ini file ok? Hi Steve, sorry for not getting back to you. I hadn't realized there was a question here when I originally skimmed the email. This can be done in lib/galaxy/config.py My next question is based on permissions. It looks like galaxy has to own the file (as nobody in your example) to upload and remove it from the directory. I'd like to change it to be more forceful, which would allow galaxy to remove the file if group owned by nobody. What module/lines do this and what impact would such a change have? This would likely have to be done in the tools/data_source/upload.py file. Thanks, I'll have a look. We are going to be working on more general methods to allow for local file uploads in typical lab environments like yours where Galaxy users have access to (at least part of) the local filesystem, which would hopefully make this less of a hack for you. That sounds very good. Basically it would be good to have file browser type functionality. We are planning on having designated areas that users can put files (or even sym links) in and see their data without uploading it. There are obviously permission issues involved in this that need some management, so I'd be interested in hearing the ideas planned. Steve ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] fastq filetypes
Is there a way to quickly determine what fastq filetype a particular fastq file is? I ask because I was recently given a fastq which which I incorrectly assumed to be fastqsanger. When I ran a fastx tool on the file, the tool seg faulted. It took me a while to figure out that the fastq type is not sanger. Is there a tool available that report what the encoding type is? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] 2011 Galaxy Community Conference, May 25-26, Lunteren, The Netherlands
Hello all, Just a reminder that the abstract submission deadline for the Galaxy Community Conference is next Monday, February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html for details. Cheers, Dave C. PS: And there is still space at the GMOD Meeting being held March 5-6 @ NESCent: http://gmod.org/wiki/March_2011_GMOD_Meeting On Tue, Feb 1, 2011 at 9:19 PM, Dave Clements clementsgal...@gmail.comwrote: Hello all, We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. *Link: http://galaxy.psu.edu/gcc2011/ * *Overview * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An Introduction to Galaxy session, offered on May 24, for Galaxy newcomers. *Registration * The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the Intro to Galaxy session) is limited and is likely to fill up before the conference itself does. *Link: http://galaxy.psu.edu/gcc2011/Register.html ** Abstract Submission * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. *Link: http://galaxy.psu.edu/gcc2011/Abstracts.html * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. *Links: http://www.nbic.nl/ and http://www.nsf.gov/ * We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ 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] Peep view for history elements broken on IE?
Hi Peter,
The error when clicking tool menu links is now fixed on galaxy-central tip.
Thanks for reporting!
On Mon, Feb 21, 2011 at 4:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has
all
been fixed on trunk by using a newer local storage library. The only IE7
issue that I am now aware of is when the tool pane is empty when using
workflows. Please let me know if you see any other issues.
Thanks,
K
On Fri, Feb 18, 2011 at 10:50 PM, Kanwei Li kan...@gmail.com wrote:
The empty tool pane issue for IE is now fixed on tip as well.
Thanks,
-K
Hi Kanwei,
I presume this was the fix for the peep view not working on IE7,
https://bitbucket.org/galaxy/galaxy-central/changeset/1dfad17e81a8
That doesn't seem to have been included in the latest galaxy-dist
release.
I've tried both main.g2.bx.psu.edu and test.g2.bx.psu.edu with
IE7 and the peep view is still unchanged. Should the test machine
be working? Perhaps there is a caching problem...
Also, when using either main.g2.bx.psu.edu or test.g2.bx.psu.edu
with IE7 I am now getting a JavaScript error when I click on any tool:
Line: 52
Error: Object doesn't support this property or method
Offending line:
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
Context:
// Log clicks on tools.
$(div.toolTitle a).click( function()
{
var tool_title = $(this).attr('id').split(-)[1];
var section_title =
$(this).parents(div.toolSectionWrapper).find(div.toolSectionTitle).text().trim();
var search_active =
$(this).parents(div.toolTitle).hasClass(search_match);
// Log action.
galaxy_async.log_user_action(tool_menu_click. + tool_title,
section_title,
JSON.stringify({search_active : search_active}));
});
This may be unrelated, but you said you'd been working on the tool
pane too, so I'm mentioning it here rather than starting a new thread
or filing a bug..
Peter
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