[galaxy-dev] (no subject)
Hello all, A lot is happening in in the Galaxy in November, and a lot of good stuff happened in October too. Take a look at the November 2014 Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_11 for the complete story, but here are some highlights: - *IRC Channel is Now Publicly Archived https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#IRC_Channel_is_Now_Publicly_Archived* - Galaxy Training Network Launched https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Galaxy_Training_Network = find a trainer near you (and sign up if you do training) - Galaxy Days: 2-3 December, Paris https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Galaxy_Days:_2-3_December.2C_Paris - Swiss German Galaxy Tour 2014 Report https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Swiss_German_Galaxy_Tour_2014_Report - Fall 2014 GUGGO Events Report https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Fall_2014_GUGGO_Events_Report - and 11 other events between now and the end of the year https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Other_Events - 38 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#New_Papers, including 3 featured papers - Who's Hiring https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Who.27s_Hiring - Two new public Galaxy Servers https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#New_Public_Servers - 35 new ToolShed repos https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#ToolShed_Contributions - And a smattering of other news https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Other_News too Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Is the new tool repositories summary in the monthly newsletter useful?
Hi Björn, A summary page of recent additions would be great, and not just for me. However, I currently get an email for every new repo and it shouldn't be hard for me to write a script to scan those emails, follow links, and generate at least a starting list of tools in wiki markup. (Should have done this a while ago.) So, if adding a summary page is easy, then please do it, but don't do it just to make creating the wiki summaries easier. Thanks, Dave C On Tue, Oct 14, 2014 at 11:45 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Dave, on IRC we had a small discussion how we can make the progress easier for you to collect this information. The idea was to create automatically Trello cards for IUC and devteam tools and maybe a summary page in the Tool Shed. Cheers, Bjoern Am 15.10.2014 um 06:52 schrieb Dave Clements: Hello all, Well, the results are unanimous: Keep it; it's worth the time invested Where to put it was far from unanimous, so we'll experiment with putting it in both the monthly newsletter and dev news briefs. Thanks all, Dave C. On Wed, Oct 8, 2014 at 9:42 AM, Dave Clements cleme...@galaxyproject.org wrote: Hi Peter, all, I've added post in both places as an option. So far we only have two responses ... Thanks, Dave C On Wed, Oct 8, 2014 at 1:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Oct 8, 2014 at 12:49 AM, Dave Clements cleme...@galaxyproject.org wrote: Hi All, The October Galaxy newsletter went out a week ago. Buried at the bottom is this 36 new ToolShed repos -- https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions which lists repositories that have been published in the Galaxy Project ToolShed in the previous month. I have two questions about this: 1. How useful is this summary? Compiling it is a manual process and it's kind of mind-numbing. Most months it takes around 2 hours (I think). I find it moderately useful, so if most Galaxy Admins think the same, it probably is overall a good time investment. 2. If we keep the summary, should we put it in the Dev News Briefs instead? I'm kinda thinking this summary is a better match for the Dev News Briefs (every release), then it is for the general newsletter (every month). I would suggest both (easy if it is just a link, a tiny bit of copy and paste if not), but that wasn't an option on the Google form. Peter -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Training Network
Hello all, We are pleased to announce the *Galaxy Training Network (GTN) https://wiki.galaxyproject.org/Teach/GTN*, a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers https://wiki.galaxyproject.org/Teach/Trainers, and to share and discover the wealth of training resources available for Galaxy. This includes training materials https://wiki.galaxyproject.org/Teach/Resources, a trainer directory https://wiki.galaxyproject.org/Teach/Trainers,best practices https://wiki.galaxyproject.org/Teach/BestPractices, and guidance on computing platforms https://wiki.galaxyproject.org/Teach/ComputingPlatforms for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community. If you teach with Galaxy, then please consider adding your organization https://wiki.galaxyproject.org/Teach/Trainers#Add_a_Trainer, materials https://wiki.galaxyproject.org/Teach/Resources#Add_a_Training_Resource, and best practices https://wiki.galaxyproject.org/Teach/BestPractices. The Trainer Directory https://wiki.galaxyproject.org/Teach/Trainers already includes 16 organizations and there may be one (or 6!) near you http://bit.ly/gxytrnmap. Thanks, The Galaxy Training Network (GTN) https://wiki.galaxyproject.org/Teach/Trainers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Is the new tool repositories summary in the monthly newsletter useful?
Hello all, Well, the results are unanimous: Keep it; it's worth the time invested Where to put it was far from unanimous, so we'll experiment with putting it in both the monthly newsletter and dev news briefs. Thanks all, Dave C. On Wed, Oct 8, 2014 at 9:42 AM, Dave Clements cleme...@galaxyproject.org wrote: Hi Peter, all, I've added post in both places as an option. So far we only have two responses ... Thanks, Dave C On Wed, Oct 8, 2014 at 1:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Oct 8, 2014 at 12:49 AM, Dave Clements cleme...@galaxyproject.org wrote: Hi All, The October Galaxy newsletter went out a week ago. Buried at the bottom is this 36 new ToolShed repos -- https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions which lists repositories that have been published in the Galaxy Project ToolShed in the previous month. I have two questions about this: 1. How useful is this summary? Compiling it is a manual process and it's kind of mind-numbing. Most months it takes around 2 hours (I think). I find it moderately useful, so if most Galaxy Admins think the same, it probably is overall a good time investment. 2. If we keep the summary, should we put it in the Dev News Briefs instead? I'm kinda thinking this summary is a better match for the Dev News Briefs (every release), then it is for the general newsletter (every month). I would suggest both (easy if it is just a link, a tiny bit of copy and paste if not), but that wasn't an option on the Google form. Peter -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Is the new tool repositories summary in the monthly newsletter useful?
Hi Peter, all, I've added post in both places as an option. So far we only have two responses ... Thanks, Dave C On Wed, Oct 8, 2014 at 1:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Oct 8, 2014 at 12:49 AM, Dave Clements cleme...@galaxyproject.org wrote: Hi All, The October Galaxy newsletter went out a week ago. Buried at the bottom is this 36 new ToolShed repos -- https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions which lists repositories that have been published in the Galaxy Project ToolShed in the previous month. I have two questions about this: 1. How useful is this summary? Compiling it is a manual process and it's kind of mind-numbing. Most months it takes around 2 hours (I think). I find it moderately useful, so if most Galaxy Admins think the same, it probably is overall a good time investment. 2. If we keep the summary, should we put it in the Dev News Briefs instead? I'm kinda thinking this summary is a better match for the Dev News Briefs (every release), then it is for the general newsletter (every month). I would suggest both (easy if it is just a link, a tiny bit of copy and paste if not), but that wasn't an option on the Google form. Peter -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Is the new tool repositories summary in the monthly newsletter useful?
Hi All, The October Galaxy newsletter went out a week ago. Buried at the bottom is this - 36 new ToolShed repos https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions which lists repositories that have been published in the Galaxy Project ToolShed in the previous month. I have two questions about this: *1. How useful is this summary?* Compiling it is a manual process and it's kind of mind-numbing. Most months it takes around 2 hours (I think). *2. If we keep the summary, should we put it in the Dev News Briefs instead?* I'm kinda thinking this summary is a better match for the Dev News Briefs (every release), then it is for the general newsletter (every month). Since we are on a survey binge, I've created a 2 question Google form for you to vote at: http://bit.ly/1qdfs5t (It has a birthday cat theme!) If you care, please vote. Discussion (in this thread) is also welcome. And many thanks to IUC for suggesting I send this email. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] October 2014 Galaxy Newsletter
Hello all, A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_10 for the complete story, but here are some highlights: - *Galaxy needs your input! https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Galaxy_Needs_Your_Input.21* You may even get rewarded for your input ... - IRC channel to be logged https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#IRC_Channel_Policy_Change, starting this month - Slides from ECCB'14 and upcoming events https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Events - 71 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Papers, including 6 featured papers - Who's Hiring? https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Who.27s_Hiring Lots of places, that's who - Two new public Galaxy Servers https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Public_Servers - New Deployment Catalog and Log Board entries https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Community_Galaxy_Hubs - 36 new ToolShed repos https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contribution - And a smattering of other news https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Other_News too Happy October! Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 2014 Galaxy Questionnaire
Hello all, The Galaxy Project is preparing for our next grant cycle and we are seeking your feedback and comments on on all things Galaxy. We have created two questionnaires, each focused on a different way to interact with Galaxy: 1. *Galaxy User Questionnaire https://docs.google.com/forms/d/1NT3ma2g7rR-mWA_vgOg2Ia_6VTFiZ86um2JhX2SecCk/formResponse* 2. *Galaxy Admin, Tool Developer, and Galaxy Developer Questionnaire https://docs.google.com/forms/d/1lszXJ2lDJ2dYCWKXBk1qT1jO7XdDDfxXmGRCUMZFX2U/viewform* Please take a few minutes and fill out the surveys that apply to you. The questionnaires are structured so you can skip topics (whole pages!) that don't apply to you, and every question is optional. *And, to thank you for your time and effort, the Galaxy Project will increase your storage quota on usegalaxy.org https://usegalaxy.org/ by 50GB. *That's a 20% increase. Let your voice be heard (and, get some storage)! The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Proposal: Create a public archive of the GalaxyProject IRC Channel
Hello all, We would like to change the logging policy for the #galaxyproject IRC channel https://wiki.galaxyproject.org/GetInvolved#IRC_Channel: - *Starting later this fall, the #galaxyproject IRC channel https://wiki.galaxyproject.org/GetInvolved#IRC_Channel will be logged online in a format that can be searched.* Currently, this channel is not logged anywhere. This change will only be made if the community agrees that a searchable online log would be an improvement. *If you have thoughts or comments on this proposal, then please post them to this Biostar thread http://bit.ly/gxybs8804*. In two weeks' time (around September 17, 2014), we'll summarize the discussion and publish a decision. *Proposal Details:* Starting sometime after community discussion ends (and assuming that discussion is favorable): 1. At least two weeks before the change: 1. Warnings will be added to the IRC channel information and on the wiki, that the log will be publicly archived as of the given start date. 2. The policy change will be announced on Galaxy Biostar https://wiki.galaxyproject.org/Support/Biostar and the Galaxy-Dev and Galaxy-Announce mailing lists https://wiki.galaxyproject.org/MailingLists. 2. On the launch date 1. The IRC channel (and the wiki) will be updated to clearly state that the IRC channel is publicly logged. 2. Announcements of the change will be posted to Biostar and the mailing lists. 3. IRC postings from the announcement onward will start showing up in the public log. 4. The IRC channel log will be included in the Galaxy search engines http://galaxyproject.org/search/. *Why now?* The project's IRC channel came up at the GalaxyAdmins BoF meetup https://wiki.galaxyproject.org/Events/GCC2014/BoFs/GalaxyAdmins at GCC2014 https://wiki.galaxyproject.org/Events/GCC2014, where it was lauded as both a great resource, *and cursed because it is not archived anywhere.* An action item from that meetup is to propose this change. The Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] September 2014 Galaxy News
Hello all, A lot of cool stuff happened in the Galaxy in August, and even more cool stuff is coming: The September Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_09 is out and here are some highlights: - Galaxy Events in Europe this Fall https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#Galaxy_Events_in_Europe.2C_Fall_2014 , *lots of 'em.* - G3: The Great GigaScience and Galaxy Workshop https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#The_Great_GigaScience_and_Galaxy_Workshop is happening Friday 19 September 2014 at The University of Melbourne. - New releases https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#New_Releases and communities https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#Galaxy-UK_Community_Launched - *lots of 'em:* - Galaxy https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#August_11.2C_2014_Galaxy_Distribution - CloudMan https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#August_2014_CloudMan_Release - BioBlend https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#BioBlend_0.5.1_Release - blend4j https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#blend4j_0.1.1_Release - *The brand new* Galaxy IPython https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#Galaxy_IPython - *And,* the Galaxy-UK Community https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#Galaxy-UK_Community_Launched was launched too. And, as always, there are new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#New_Papers, new jobs https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#Who.27s_Hiring, and a double dose of new ToolShed contributions https://wiki.galaxyproject.org/GalaxyUpdates/2014_09#ToolShed_Contributions . Happy September, Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Developer Events in Europe this Fall: Swiss-German Galaxy Tour
Hello all, The *2014 Swiss-German Galaxy Tour https://wiki.galaxyproject.org/Events/SG2014* is happening from 30 September through 2 October. The tour features 3 events and they will all be great ways to meet fellow developers, and learn more about defining tools and deploying and administering Galaxy. Space is limited at all these events, so if you are interested, *you are strongly encouraged to register now*. The tour is organized (and hosted) by Hans-Rudolf Hotz and Björn Grüning. The events are: *Galaxy Training and Demo Day https://wiki.galaxyproject.org/Events/Switzerland2014/trainingday* 30 September Bern, Switzerland *(second Swiss) Galaxy Workshop https://wiki.galaxyproject.org/Events/Switzerland2014 * 1 October Bern, Switzerland *German Galaxy Developers Day https://wiki.galaxyproject.org/Events/Germany2014 * 2 October Freiburg, Germany There are also several events for Galaxy Users planned this fall. See the Galaxy Events page https://wiki.galaxyproject.org/Events for more. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] August 2014 Galaxy Newsletter
Hello all, The August 2014 Galaxy Update Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_08 is out. Here's a preview of what's inside: - GCC2015 will be held in Norwich, United Kingdom, 6-8 July 2015 https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#GCC2015:_Norwich.2C_United_Kingdom.2C_6-8_July_2015 - GCC2014 was a tremendous success https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#GCC2014_Report. Watch the talks, review the slides, posters, and BoF writeups. - ISMB and BOSC 2014 slides, posters and videos https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#Galaxy_.40_ISMB_and_BOSC_2014_Slides_and_Posters too. - 53 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#New_Papers - One new public server (IM-PET) https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#New_Public_Servers - Who's hiring? https://wiki.galaxyproject.org/GalaxyUpdates/2014_08#Who.27s_Hiring It turns out that lots of places are. Happy August, Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 2014 Galaxy Community Conference June 6 Registration Deadline (this Friday)
Hello all, Regular registration for the 2014 Galaxy Community Conference (GCC2014, https://wiki.galaxyproject.org/Events/GCC2014) closes this Friday, June 6. After that late registration is still open, but registration rates *go up 100%.* GCC2014 is all about high-throughput biology. It's in Baltimore, from June 30 through July 2. The full program is posted, and includes - Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay - 15 sessions on 12 topics in 5 parallel tracks with topics ranging from *Visualizing NGS data *to* Galaxy installation and administration* - 26 talks https://wiki.galaxyproject.org/Events/GCC2014/Program#Day_1:_Main_Meeting.2C_July_1 including a keynote by Steven Salzberg, and 25 other talks by researchers and industry leaders - 25 Posters https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Poster_Abstracts - and counting - we still have space for a few more https://wiki.galaxyproject.org/Events/GCC2014/Abstracts#Abstract_Submission - Lightning Talks - Present your rsesarch in two fast paced sessions. - Birds-of-a-Feather https://wiki.galaxyproject.org/Events/GCC2014/BoFs - Gather with other researchers with common interests and challenges (and propose one https://wiki.galaxyproject.org/Events/GCC2014/BoFs#Want_to_plan_a_BoF.3F for your own area of interest) - The first ever GCC Hackathon https://wiki.galaxyproject.org/Events/GCC2014/Hackathon (only 8 spaces left) Please do let us know if you have any questions. We would love to see you in Baltimore. Thanks, Dave Clements *2014 Galaxy Community Conference (GCC2014) http://galaxyproject.org/GCC2014*http://galaxyproject.org/GCC2014 June 30 - July 2, 2014 Homewood Campus http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ Johns Hopkins University http://jhu.edu/Baltimore, Maryland http://visitors.baltimorecity.gov/, United States -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] June 2014 Galaxy Update Newsletter: GCC2014 registration closes in 1 week!
Hello all, The June 2014 Galaxy Update Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_06 is out! There's a lot going on in the project and the community right now. The big news for the coming month is - *GCC2014 registration closes June 6! https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_July_2.2C_Baltimore* - (OK, that's a lie, but after June 6, late registration rates kick in, and you really don't want to pay those.) - *GCC2014 starts June 30 https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#GCC2014:_June_30_-_July_2.2C_Baltimore!* - *The first ever GCC Hackathon starts June 28 https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Hackathon_at_GCC2014!* - After a very long and productive life, the *Galaxy-User mailing list is retiring on June 6* https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Retired_June_6. (Don't worry. It's been replaced by Galaxy Biostar https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy-User_Being_Retired_June_6 .) There are also at least 14 other Galaxy related events https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Other_Events in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil. And, in the past month there were: - 49 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Papers - One new public server (deepTools) https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#New_Public_Servers - One new Galaxy deployment description (deepTools) https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#Galaxy_Community_Hubs - and a stunning number of ToolShed contributions https://wiki.galaxyproject.org/GalaxyUpdates/2014_06#ToolShed_Contributions Please let us know if you have anything to include in the July newsletter, and we will see you in Baltimore! Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2014 Early Registration closes this Friday, May 23
Hello all, This just a reminder that early registrationhttps://wiki.galaxyproject.org/Events/GCC2014/Register for the 2014 Galaxy Community Conference (GCC2014)https://wiki.galaxyproject.org/Events/GCC2014 *closes this Friday, May 23* Register early and *avoid paying 70% more for regular registration costs.* Early registration is downright affordable, with combined registration (Training Dayhttps://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registering early assures you a place at the conference and also a spot in the Training Day workshopshttps://wiki.galaxyproject.org/Events/GCC2014/TrainingDayyou want to attend. And ... - The program https://wiki.galaxyproject.org/Events/GCC2014/Program , and abstracts https://wiki.galaxyproject.org/Events/GCC2014/Abstracts for all accepted talks are now available. - Registration for the GCC2014 hackathonhttps://wiki.galaxyproject.org/Events/GCC2014/Hackathon is also open (and also has limited capacity - register for that now toohttps://wiki.galaxyproject.org/Events/GCC2014/Hackathon ) - We are pleased to have Penguin Computinghttp://www.penguincomputing.com/as a Silver Sponsor for GCC2014 You are strongly encouraged to register this week. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Thanks a bunch, and hope to see you in Baltimore! Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2014 Poster Abstracts due April 25, THIS FRIDAY
Hello all, This is just a reminder that poster abstracts for the 2014 Galaxy Community Conference (GCC2014) *are due this Friday. * Abstracts can be submitted at https://wiki.galaxyproject.org/Events/GCC2014/Abstracts Note that posters are reviewed and accepted on a rolling basis, until all slots are full. The deadline is this Friday but sooner may be better. In other news: - We are delighted to have Steven Salzberg as the keynote speakerhttps://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker . - Registration for the GCC2014 hackathonhttps://wiki.galaxyproject.org/Events/GCC2014/Hackathonis now open - Early registrationhttps://wiki.galaxyproject.org/Events/GCC2014/Registerfor the GCC2014 Training Day and Meetinghttps://wiki.galaxyproject.org/Events/GCC2014/Programare also open - Abstracts https://wiki.galaxyproject.org/Events/GCC2014/Abstractsfor accepted talks will start showing up on the website this week. Thanks, and hope to see you in Baltimore, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, *We are pleased to announce that Early Registration https://wiki.galaxyproject.org/Events/GCC2014/Register and Talk and Poster Abstract Submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts are now open for the 2014 Galaxy Community Conference (GCC2014) https://wiki.galaxyproject.org/Events/GCC2014.* GCC2014 https://wiki.galaxyproject.org/Events/GCC2014 will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/of Johns Hopkins University http://jhu.edu, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. GCC2014https://wiki.galaxyproject.org/Events/GCC2014starts with a Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay *Early registration https://wiki.galaxyproject.org/Events/GCC2014/Register* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics pagehttps://wiki.galaxyproject.org/Events/GCC2014/Logisticsfor details on this and other housing options. *Abstract submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience http://www.gigasciencejournal.com/* Galaxy: Data Intensive and Reproducible Research series announced for the last conference has published its first papershttp://www.gigasciencejournal.com/series/Galaxy, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest updatehttp://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committeehttps://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] April 2014 Galaxy Update Newsletter: GCC2014 Talk Abstracts due this Friday
Happy April everyone! It's a busy time in the Galaxyhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04 and that is reflected in the April 2014 Galaxy Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04. First, there were a record 63 new papershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#New_Papers in the past month, six of which we have highlightedhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#New_Papers (also a record). Three new public Galaxy servershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#New_Public_Servers, and one Galaxy Community Log Board entryhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Galaxy_Community_Hubs were also added in March. However, the big news this month is Upcoming Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Events : - Abstract submission for oral presentationshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Oral_Presentation_Abstract_Submission_Closes_April_4 at the 2014 Galaxy Community Conference (GCC2014)https://wiki.galaxyproject.org/GalaxyUpdates/2014_04#GCC2014:_June_30_-_July_2.2C_Baltimore closes this Friday, April 4https://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Oral_Presentation_Abstract_Submission_Closes_April_4 . - Early Registrationhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Registration_is_Open for GCC2014https://wiki.galaxyproject.org/GalaxyUpdates/2014_04#GCC2014:_June_30_-_July_2.2C_Baltimore is open. Register now to secure your spot and save a bundle. - Globus World 2014https://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Globus_World_2014 is coming up April 15-17, in Chicago. Globus Genomics will have a strong presence. - Registration for the UC Davis 2014 Bioinformatics Workshophttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#UC_Davis_2014_Bioinformatics_Workshop is also open. - And there are lots of other eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Other_Events to keep us all out of trouble for the next few months. And as always, there are new ToolShed contributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#ToolShed_Contributions and other newshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_04#Other_News as well. If you have anything you would like to see in the next *Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Dave Clements and the Galaxy Teamhttps://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GCC2014 Early Registration and Abstract Submission are now OPEN!
Hello all, This is just a reminder that *abstract submission for oral presentations at GCC2014 closes April 4*, ten days from now. This is a great opportunity to present your work. See https://wiki.galaxyproject.org/Events/GCC2014/Abstracts for details and how to submit. Thanks, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, *We are pleased to announce that Early Registration https://wiki.galaxyproject.org/Events/GCC2014/Register and Talk and Poster Abstract Submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts are now open for the 2014 Galaxy Community Conference (GCC2014) https://wiki.galaxyproject.org/Events/GCC2014.* GCC2014 https://wiki.galaxyproject.org/Events/GCC2014 will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/of Johns Hopkins University http://jhu.edu, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. GCC2014https://wiki.galaxyproject.org/Events/GCC2014starts with a Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay *Early registration https://wiki.galaxyproject.org/Events/GCC2014/Register* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics pagehttps://wiki.galaxyproject.org/Events/GCC2014/Logisticsfor details on this and other housing options. *Abstract submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience http://www.gigasciencejournal.com/* Galaxy: Data Intensive and Reproducible Research series announced for the last conference has published its first papershttp://www.gigasciencejournal.com/series/Galaxy, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest updatehttp://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committeehttps://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] BOSC 2014 Call for Abstracts
Hello all The call for abstracts for BOSC 2014 is out. See below for details. If you have questions I'm sure that Peter, Brad, Chris, and Hans-Rudolf, all frequent contributors to this list, would be answer them. And glad to see that GigaScience, a GCC sponsor, is also sponsoring BOSC this year. Cheers, Dave C. Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014) A Special Interest Group (SIG) of ISMB 2014 Dates: July 11-12, 2014 Location: Boston, MA, USA Web site: http://www.open-bio.org/wiki/BOSC_2014 Email: b...@open-bio.org BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce Important Dates: March 24, 2014: Registration opens for ISMB and BOSC (https://www.iscb.org/ismb2014-registration) April 4, 2014: Deadline for submitting BOSC abstracts (http://www.open-bio.org/wiki/BOSC_Abstract_Submission) May 1, 204: Notification of accepted talk abstracts emailed to authors July 9-10, 2014: Codefest 2014, Boston (http://www.open-bio.org/wiki/Codefest_2014) July 11-12, 2014: BOSC 2014, Boston (http://www.open-bio.org/wiki/BOSC_2014) July 11-15, 2014: ISMB 2014, Boston The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. BOSC is sponsored by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Scien! ce within the biological research community. We invite you to submit one-page abstracts for talks and posters. This year's session topics are: Open Science and Reproducible Research Software Interoperability Genome-scale Data and Beyond Visualization Translational Bioinformatics Bioinformatics Open Source Libraries and Projects Once again we thank Eagle Genomics for sponsoring the BOSC Student Travel Awards, and welcome the open access journal GigaScience as a new sponsor for BOSC 2014. BOSC 2014 Organizing Committee: Nomi Harris and Peter Cock (co-chairs), Raoul Jean Pierre Bonnal, Brad Chapman, Robert Davey, Christopher Fields, Hans-Rudolf Hotz, Hilmar Lapp ___ Members mailing list memb...@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/members ___ Biopython mailing list - biopyt...@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biopython -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] March 2014 Galaxy Update Newsletter
Hello all, Find out what's happening in the Galaxyhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03 ! The March 2014 Galaxy Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03 include is out and highlights include: - 54 new papershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#New_Papers - Who's hiringhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Who.27s_Hiring - Upcoming Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Events, including - Galaxy Australasia Workshop 2014 (GAW 2014): 24-25 Marchhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Galaxy_Australasia_Workshop_2014:_24-25_March - Globus World 2014https://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Globus_World_2014, April 15-17 - Registrationhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Registration_is_Open and abstract submissionhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Abstract_Submission_is_Open for the 2014 Galaxy Community Conference (GCC2014)https://wiki.galaxyproject.org/GalaxyUpdates/2014_03#GCC2014:_June_30_-_July_2.2C_Baltimore are open - One new and one returning public Galaxy serverhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#New_Public_Servers - Feb 10, 2014 Galaxy Distributionhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Galaxy_Distributions - Tool Shed Contributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#ToolShed_Contributions - Other Newshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_03#Other_News If you have anything you would like to see in the next *Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Thanks, Dave Clements and the Galaxy Teamhttps://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2014 Early Registration and Abstract Submission are now OPEN!
Hello all, *We are pleased to announce that Early Registration https://wiki.galaxyproject.org/Events/GCC2014/Register and Talk and Poster Abstract Submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts are now open for the 2014 Galaxy Community Conference (GCC2014) https://wiki.galaxyproject.org/Events/GCC2014.* GCC2014 https://wiki.galaxyproject.org/Events/GCC2014 will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/of Johns Hopkins University http://jhu.edu, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. GCC2014https://wiki.galaxyproject.org/Events/GCC2014starts with a Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay *Early registration https://wiki.galaxyproject.org/Events/GCC2014/Register* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics pagehttps://wiki.galaxyproject.org/Events/GCC2014/Logisticsfor details on this and other housing options. *Abstract submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience http://www.gigasciencejournal.com/* Galaxy: Data Intensive and Reproducible Research series announced for the last conference has published its first papershttp://www.gigasciencejournal.com/series/Galaxy, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest updatehttp://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committeehttps://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] February 2014 Galaxy Update Newsletter
Hello all, The 25th Edition of Galaxy Update is outhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02. Highlights from the February 2014 Galaxy Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02 include: - 42 new papershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#New_Papers - Who's hiringhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Who.27s_Hiring - Upcoming Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Events, including - Registration for GCC2014 opens February 10https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#GCC2014:_June_30_-_July_2.2C_Baltimore - Registration for the Galaxy Australasia Workshop 2014 (GAW 2014)https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Australasia_Workshop_2014_.28GAW_2014.29 and GMOD Malaysia 2014https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#GMOD_Malaysia_2014 are open. - Three new public Galaxy servershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#New_Public_Servers - January 2014 CloudMan Releasehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Distributions - New Galaxy Deployment Cataloghttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Community_Hubs and Community Log Boardhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_Community_Hubs entries - Tool Shed Contributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#ToolShed_Contributions - Johns Hopkins and George Washington walk into a bar ...https://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Galaxy_is_now_at_Johns_Hopkins_and_GWU_.28and_Penn_State.21.29 - Other Newshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02#Other_News If you have anything you would like to see in the next *Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Dave Clements and the Galaxy Teamhttps://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Remote User Logout
Hi Eric, I figured this was as good of a time as any... I moved the AD/LDAP/External authentication out of the Apache Proxy page (who would think to look there?) and into its own page. I added my organisation's information on mod_auth_kerb while I was at it. That seemed like a reasonable place to put this sort of information. I've also reduced the solution to just the necessary portions, but it would need to be tested by someone. https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases#Logging_out_Basic_Auth.27d_Users Thanks for updating the admin wiki pages. The admin wiki pages are sprawling and any efforts to keep them current and well organized are *dearly appreciated*. I suggest we re-link the community log page to that subsection as it has more related information, if that is amenable to everyone. I've updated https://wiki.galaxyproject.org/Community/Log/2014/LDAPRemoteUserLogout and added links to the two wiki pages. I left the content on the log page, although I'm not at all certain that is wise: The log pages are meant to be a quick and easy way to document stuff and make it easy to find. I think that leaving this log page (mostly) as it was will encourage contribution more than stripping it. Most people are not going to be willing to locate the right pages in the wiki for all their content. However, I'm hoping that if they can just drop content into one, time-stamped, no-commitment-to-keep-it-current, place then they will be way more likely to contribute. That's my theory anyway. So far, my theory hasn't particularly panned out, but the log board is still less than 2 months old. Thanks again, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Remote User Logout
Hi Eric, Tim, Hi Tim, Amazing! Thank you for sharing that code. That'll save me some work when I get around to implementing it on my galaxies. I'll add a Wiki page for it later today, lest this knowledge be lost to the mailing list. That is an excellent suggestion. I've created a log board entry for it.: https://wiki.galaxyproject.org/Community/Logs The first for 2014. Feel free to edit, or send me revisions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Australasia Workshop (GAW 2014), 24-25 March, Melbourne
Hello all, *We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW 2014) https://wiki.galaxyproject.org/Events/GAW2014 will be held in Melbourne, Australia on 24 and 25th March 2014.* The Galaxy Australasia Workshophttps://wiki.galaxyproject.org/Events/GAW2014 is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch http://wp.csiro.au/css/ in Melbourne. GAW 2014 will also include poster session, keynote speakers. *You should attend to:* - Present your work! - Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets. - Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them. - Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction. - Learn - how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics) - how to share, publish, and reuse your analyses with Galaxy - how to perform and enable your users to perform common, yet complex, analyses using Galaxy - when and how to use Galaxy on the Cloud *Topics will potentially include:* - Image analysis and processing using Galaxy. - RNAseq/ChIPseq/Variant Calling/RNA Quality Control. - Galaxy on the Research Cloud. - CSIRO galaxy service - partnership between science and IT. - Identifying proteins from mass spec data with Galaxy. *Call For Abstracts* Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit a brief one-page abstract and brief one-paragraph bio to the GAW2014 Organisers gaw2014-...@groups.galaxyproject.org *by February 15th, 2014.* Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance. Submissions should clearly state whether they are for: poster or oral presentation. Looking forward to seeing you all in Melbourne! GAW 2014 Organising Committeehttps://wiki.galaxyproject.org/Events/GAW2014#Organising_Committee -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] January 2014 Galaxy Update Newsletter
Hello all, The January 2014 Galaxy Update is outhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01 ! - Galactic Hubs!https://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Galaxy_Community_Hubs - Galaxy Community Log Boardhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Galaxy_Community_Log_Board: Share your Galaxy experience - Galaxy Deployment Cataloghttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Galaxy_Deployment_Catalog: Describe your local install so others can learn from it. - 2013 Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#A2013_Events_Archive *and presentation https://wiki.galaxyproject.org/GalaxyUpdates/2014_01#A2013_Events_Archive* archive - 52 new papershttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#New_Papers - Who's hiringhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Who.27s_Hiring - Upcoming Eventshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Events, including - GCC2014: June 30 - July 2, Baltimorehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#GCC2014:_June_30_-_July_2.2C_Baltimore - Training Day Topic Voting, January 6-17https://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Training_Day_Topic_Voting.2C_January_6-17 - Sponsorshipshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Sponsorships and Exhibitorshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Exhibitors - 2013 Galaxy Day Reporthttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#A2013_Galaxy_Day_Report - CAPER https://wiki.galaxyproject.org/GalaxyUpdates/2014_01#CAPER, a new public Galaxy serverhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#New_Public_Servers - Distributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Galaxy_Distributions - Tool Shed Contributionshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#ToolShed_Contributions - Other Newshttps://wiki.galaxyproject.org/GalaxyUpdates/2014_01#Other_News If you have anything you would like to see in the next *Galaxy Update https://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Best wishes to you and yours for a happy and spectacular 2014, Dave Clements and the Galaxy Teamhttps://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GCC2014 Training Day: Topic Nomination is now open
Hello all, Just a reminder that GCC2014 Training Day Topic Nominations close this Friday, December 20. We have 9 excellent nominations thus farhttp://wiki.galaxyproject.org/Events/GCC2014/TrainingDay, but we need more. If you have something you want to see covered, *then please nominate a topic http://bit.ly/gcc2014tdnom before the end of this Friday.* Thanks, Dave C, on behalf of the GCC2014 Organizing Committee On Mon, Dec 2, 2013 at 10:32 AM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, Training Day topics are nominated by you http://bit.ly/gcc2014tdnom, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay , - what topics were nominated in 2013 http://bit.ly/1i2j1gN, and - the Events http://wiki.galaxyproject.org/Events and the Events Archive http://wiki.galaxyproject.org/Events/Archive pages. Nominated topics will be published on the Training Dayhttp://wiki.galaxyproject.org/Events/GCC2014/TrainingDay page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! http://bit.ly/gcc2014tdnom Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. See you in Baltimore! GCC2014 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2014/Organizers --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)http://galaxyproject.org/gcc2014will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ of Johns Hopkins University http://jhu.edu/, inBaltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Announcing the Galaxy Community Log Board
Hello all, I am pleased to announce the *Galaxy Community Log Board http://wiki.galaxyproject.org/Community/Logs.* The Log Board is a place to share how you addressed a particular task in your Galaxy deployment. Log entries describe specific solutions to particular tasks, such as the details of what steps were taken to deploy Galaxy on particular platformshttp://wiki.galaxyproject.org/Community/Log/2013/URGIVirtualisation, or specific stumbling blocks when configuring Galaxyhttp://wiki.galaxyproject.org/Community/Log/2013/Example. Solutions can be described on this wikihttp://wiki.galaxyproject.org/Community/Log/2013/Example, or just some metadata and a link to the description elsewherehttp://wiki.galaxyproject.org/Community/Log/2013/UsingBioServicesWithGalaxy. Log entries are an easy way to help others (and learn from others) by sharing what you've already done. If you have figured out or documented how to do something, then this is the ideal forum for sharing that information with the community. Share your experiencehttp://wiki.galaxyproject.org/Community/Logs#Add_a_Log_Page *now http://wiki.galaxyproject.org/Community/Logs#Add_a_Log_Page.* The Galaxy Community Log Boardhttp://wiki.galaxyproject.org/Community/Logs describes how things can be done, and it complements the (also recently announced http://wiki.galaxyproject.org/News/GalaxyDeploymentCatalog) *Galaxy Deployments Catalog http://wiki.galaxyproject.org/Community/Deployments*, which describes different Galaxy installations. Both the Log Boardhttp://wiki.galaxyproject.org/Community/Logs and the Deployments Cataloghttp://wiki.galaxyproject.org/Community/Deployments came out of discussions at the GCC2013 GalaxyAdmins Birds-of-a-Feather gathering http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins. Thanks to everyone who attended that BoF. Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Announcing the Galaxy Deployment Catalog!
Hello all, *I am pleased to formally announce the Galaxy Deployment Catalog http://wiki.galaxyproject.org/Community/Deployments*, a place to describe individual Galaxy deployments, and to learn how others in the community are implementing Galaxy in production environments. If you have a Galaxy deployment then please take a few minutes to describe your instance to the community. There are two ways to do this. *Use the Wiki Template* Go to the Using the Wiki section of the catalog home pagehttp://wiki.galaxyproject.org/Community/Deployments#Using_the_Wiki, enter a CamelCase name for your deplloyment, click Create ..., and then edit, preview, and save the page. Voilà, an entry for your deployment now exists in the catalog. *Use the Google Form* Fill out this Google Form http://bit.ly/gxydeployform. In a week or two, a deployment catalog page will be programmatically created and you will receive an email. The wiki method requires a wiki login, but gives you control over how the page appears. The Google form is easier. Thanks a bunch, and please let me know if you have any questions. Dave C. PS: The form submission method was inspired by (stolen from?) Philip Moncuquet's post http://dev.list.galaxyproject.org/survey-td4662749.html earlier this week. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2014 Training Day: Topic Nomination is now open
Hello all, Training Day topics are nominated by you http://bit.ly/gcc2014tdnom, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay , - what topics were nominated in 2013 http://bit.ly/1i2j1gN, and - the Events http://wiki.galaxyproject.org/Events and the Events Archivehttp://wiki.galaxyproject.org/Events/Archive pages. Nominated topics will be published on the Training Dayhttp://wiki.galaxyproject.org/Events/GCC2014/TrainingDay page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! http://bit.ly/gcc2014tdnom Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. See you in Baltimore! GCC2014 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2014/Organizers --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)http://galaxyproject.org/gcc2014will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ of Johns Hopkins University http://jhu.edu/, inBaltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] survey
Hello Philip, all I'm working on a complementary effort that I was going to announce later this week, but maybe I'll just introduce it now. Something that came out of the GalaxyAdmins meetup in Oslo was a desire for some way for the community to describe the details of their Galaxy deployments to a wider audience. This would allow newcomers to find out what others have done, and for existing deployments to find out who else is doing something similar. To meet that need, this wiki infrastructure was created: http://wiki.galaxyproject.org/Community/Deployments This includes sections on user community, but is not as detailed as the survey. I have a couple of requests: 1. Philip, is it possible to add another question to the form: Can this information be posted to the Galaxy Deployments Cataloghttp://wiki.galaxyproject.org/Community/Deployments ? with a default of no. For any yes responses, you could send me the info and I could create a basic entry. 2. I second Phillip's request. Please do give him a few minutes and fill out the survey. I'll make sure the summary gets posted to the wiki. 3. Please give some thought to also creating a deployment page. Instructions are on the wiki. Thanks a bunch, Dave C. PS: This complements http://wiki.galaxyproject.org/Community/Logs which I actually will announce later this week. Any feedback on either is welcome. On Mon, Dec 2, 2013 at 2:14 PM, Philippe Moncuquet philippe.m...@gmail.comwrote: Hi, I hope this is relevant to the dev list but if it is not please let me know. I was trying to estimate active users out of our registered users. I ended counting users that had a job during the last month. How would you guys do ? During this process I also wanted to see how we were doing in comparison to other instance. I set up a simple survey and would greatly appreciate if instance admin would take 2 min to complete it. I will publish results here (or maybe to some more relevant place, let me know) at the end of the month. https://fr.surveymonkey.com/s/CD6NN88 Regards, Philip ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] December 2013 Galaxy Update
Hello all, The final *Galaxy Update* newsletter of 2013http://wiki.galaxyproject.org/GalaxyUpdates/2013_12 is out: - Three new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#A50.2B-_Public_Servers , *bringing the total to over 50.* - 61 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#New_Papers (a new monthly record) - Who's hiringhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Who.27s_Hiring at seven different institutions - Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Events, including - Save these dates! GCC2014: June 30 - July 2, Baltimorehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#GCC2014:_June_30_-_July_2.2C_Baltimore - Sponsorshipshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Sponsorships and Exhibitorshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Exhibitors - UC Davis Bioinformatics Boot Campshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#UC_Davis_Bioinformatics_Boot_Camps - Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Galaxy_Distributions - Tool Shed contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#ToolShed_Contributions (including a new ToolShedhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#New_Public_ToolSheds ) - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Other_News If you have anything you would like to see in the next *Galaxy Update http://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Thanks for an excellent year, Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Next GalaxyAdmins Meetup: November 20
Hello all, Just a reminder that there is a GalaxyAdmins meetup on Wednesday November 20 (tomorrow) at 10am US Central time. See http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20 Nate Coraor will talk about the move of usegalaxy.org to TACC, and Srinivas and myself will talk about followup to the GalaxyAdmins Birds-of-a-feather session at GCC2013. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pageshttp://wiki.galaxyproject.org/Community/Deployments 2. Galaxy Log Pages http://wiki.galaxyproject.org/Community/Logs Please come prepared to discuss what you would like to see in these pages, and make suggestions on how to make it easy to create these documents. Finally, it takes a few minutes to connect to the meetup technology. Please give yourself 5 or 10 minutes in advance to connect. Thanks, Dave C On Thu, Nov 14, 2013 at 12:00 AM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup pagehttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20 for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pageshttp://wiki.galaxyproject.org/Community/Deployments 2. Galaxy Log Pages http://wiki.galaxyproject.org/Community/Logs And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] wiki contributions: Admin/Config/ProFTPd_with_AD
Hi Eric, I've pasted the text into the http://wiki.galaxyproject.org/Admin/Config/ProFTPd_with_AD page. I used the Apache syntax highlighter for the ProFTPd configuration file snippets, which I'm pretty sure is not exactly right, but I'm guessing it's close enough. To unlock a page for editing you need to create an account, login, and then edit the page. This is a big pain until your account becomes *vetted*. Until then you have to answer Galaxy trivial pursuit questions on every save. We vet accounts on request, or once a month, whichever happens sooner. Thanks for contributing this, Dave C On Thu, Nov 14, 2013 at 1:03 PM, Eric Rasche rasche.e...@yandex.ru wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I'd like to contribute what I've learnt today to this particular page. As it is locked, I am unsure how to contribute my information, so I'm posting here in the hopes that someone with rights will update it. Formatted in (pandoc compatible) Markdown for your ease. # Configuring ProFTPD with OpenLDAP I've found a set of working options for using ProFTPD with OpenLDAP servers (instead of AD). This configuration file can be modified and placed in `/etc/proftpd/conf.d/galaxy.conf Using the /conf.d/ directory, you can allow the ProFTPd to serve both local users (with PAM authentication) in the main configuration file, AND galaxy users on another port. ``` VirtualHost xxx.yyy.zzz RequireValidShell off Usergalaxy Group galaxy Umask 137 027 AllowOverwrite on # Ensure auth is LDAP AuthPAM off AuthOrder mod_ldap.c # Serve this VirtualHost on port 4000 Port4000 # LDAP Bind information LDAPServer ldaps://xxx.yyy.zzz/??sub LDAPUsers ou=People,dc=yyy,dc=zzz (uid=%u) LDAPAuthBinds on # Force those numbers even if LDAP finds a valid UID/GID LDAPDefaultUID 1003 LDAPDefaultGID 1003 LDAPForceDefaultUID on LDAPForceDefaultGID on # Please generate home dir with user/group rwx permissions. Could probably be stricter CreateHome on 770 LDAPGenerateHomedir on 770 # Force this homedir even if LDAP said something different LDAPForceGeneratedHomedir on LDAPGenerateHomedirPrefix /home/galaxy/galaxy/database/ftp/%u...@cpt.tamu.edu # The username is already incorporated in the %u, use this or it will get appended again LDAPGenerateHomedirPrefixNoUsername on TransferLog /var/log/proftpd/xfer-galaxy.log # Cause every FTP user to be jailed (chrooted) into their home directory DefaultRoot /home/galaxy/galaxy/database/ftp/%u...@cpt.tamu.edu # Allow users to resume interrupted uploads AllowStoreRestart on # I set these as my passive ports because I run a very strict firewall. Change as needed PassivePorts49152 5 /VirtualHost ``` Notably, this configuration allows a galaxy virtualhost to coexist with the normal FTP capabilities provided by ProFTPd, so users can still access their home directories AND galaxy users can upload to galaxy. Authentication can of course be changed to suit one's needs. # TLS Configuration If you're running the galaxy FTP portion under a VirtualHost, like described above, you'll notice that TLS directives placed in the main proftpd.conf file do not apply to VirtualHosts. As such, you can add a section that looks like this to every VirtualHost that needs to be secured ``` IfModule mod_tls.c TLSEngine on TLSLog /var/log/proftpd/tls.galaxy.log # Your cert and private key TLSRSACertificateFile /etc/ssl/certs/my.crt TLSRSACertificateKeyFile/etc/ssl/private/my.key TLSCACertificateFile/etc/ssl/certs/ca.bundle # I've found that this is required for FileZilla TLSOptionsNoCertRequest EnableDiags NoSessionReuseRequired # Most clients won't be sending certs TLSVerifyClient off TLSRequired on /IfModule ``` Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJShTqNAAoJEMqDXdrsMcpVZh8QAL1PvZTtTco+hBeJ+2o9jCyp DpasNtMm0PTKjmBR7Cq5lxNJeGlAcAJmafGKxnf7EEGPhJnw8xWUDwGolmjJmzik
[galaxy-dev] Next GalaxyAdmins Meetup: November 20
Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup pagehttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20 for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pageshttp://wiki.galaxyproject.org/Community/Deployments 2. Galaxy Log Pages http://wiki.galaxyproject.org/Community/Logs And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] November 2013 Galaxy Update Newsletter
Hello all, The November 2013 Galaxy Update is outhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11 : *Highlights:* - Two new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Public_Servers : CoSSci: Complex Social Science Gatewayhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#CoSSci:_Complex_Social_Science_Gateway (which has *nothing* to do with biology), and BioCiphers Lab Galaxyhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#BioCiphers_Lab_Galaxy . - 53 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#New_Papers, including Expanding roles in a library-based bioinformatics service program: a case study, DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data, and Ten Simple Rules for Reproducible Computational Research - Who's hiringhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Who.27s_Hiring - Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Other_Events, including - Save these dates! GCC2014: June 30 - July 2, Baltimorehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#GCC2014:_June_30_-_July_2.2C_Baltimore - Galaxy Day, December 4, Parishttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Galaxy_Day.2C_December_4.2C_Paris - UC Davis Bioinformatics Boot Campshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#UC_Davis_Bioinformatics_Boot_Camps - Lifeportal launched at the University of Oslohttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Lifeportal_at_the_University_of_Oslo - Tool Shed contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_11#Tool_Shed_Contributions If you have anything you would like to see in the next *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Please save these dates! GCC2014: June 30 - July 2
Hello all, The 2014 Galaxy Community Conference (GCC2014)http://wiki.galaxyproject.org/Events/GCC2014 has been scheduled for June 30 through July 2, at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/ of Johns Hopkins University http://jhu.edu/, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference will also includes a*Training Day* offering in-depth topic coverage, across several concurrent sessions. See the GCC2013 web sitehttp://wiki.galaxyproject.org/Events/GCC2013 for an idea of what happens at a Galaxy Community Conference. See you next summer, GCC2014 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] August 2013 Galaxy Update Newsletter is out
Hi Samuel, everyone, There is now a Vimeo channel containing all 25 taped talks from GCC2013: https://vimeo.com/channels/581875 We're still figuring out how to best use Vimeo. Please do let us know if you have any suggestions for how to improve the site. Look for more content here going forward. And it's on a Vimeo Plus account, so you won't see any ads for phones, football teams, telescopes, or faster than light travel. :-) Dave C On Mon, Aug 12, 2013 at 12:28 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hi Samuel, everyone, Our main reason for avoiding these ad supported services is that we don't want people to have to deal with ads to see Galaxy Video content. Dave C On Sat, Aug 10, 2013 at 2:54 AM, Samuel Lampa samuel.la...@gmail.comwrote: On 08/08/2013 07:38 PM, Dave Clements wrote: I wanted to ask though, are there specific reasons for not using a service like YouTube / Vimeo etc? Yes! Um, but I can't remember what they are (sadly, this is true). We'll talk about this on the next outreach call, and I'll post here what we decide. Ok, nice, many thanks! Best Regards // Samuel -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Creating Galaxy Admin / Local Install Mailing List - Updates?
Hi Hans-Rudolf, Adam, As the BoF page indicates, we decided not to do this, for the reasons listed on the page. So, for now, we won't create a separate email list, or use MailMan topics (which I had high hopes for). However, we may not be done with this yet. The plan is still to move Galaxy-User to the BioStar forum platform. At that point we will take a hard look at implementing a Galaxy-Admin forum in BioStar. As for the September 2013 GalaxyAdmins meetup - it is not going to happen. This is entirely because I dropped the ball. Unfortunately, I'm not optimistic about having one in October either, as I'll be doing workshops in South Africa for much of that month. However, if someone wants to take the lead for lining up content for a September or October meetup please step forward now and Srinivas and I will do what we can to make it happen. Thanks, Dave C On Thu, Sep 12, 2013 at 2:12 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Adam I guess the latest is written down in the notes for the GalaxyAdmins BoF at GCC2013, see: http://wiki.galaxyproject.org/**Events/GCC2013/BoF/**GalaxyAdminshttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins maybe we can discuss this again at the next 'meetup'? The next 'meetup' is scheduled for September 18, but I don't know whether it will happen? I am sure Dave will know more. Regards, Hans-Rudolf On 09/12/2013 04:52 AM, Adam Brenner wrote: Howdy, I know this has been discussed before, but I can not find the email threads on this...but what was the status on creating a galaxy admin / local install mailing list? The Devel list is very chatty and while my filters do a good job, I think it will be easier for others to find help on their own if it was on a separate mailing list It would be easier to search and look back at previous threads. However, the added benefit of having the devel list is that we get feedback from Galaxy Developers As the saying godes: Just food for thought, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Statistical Genomics Post-doctoral Position in Makova Lab at Penn State
Hello all, There's a post-doc opening in the Makova Lab at Penn State. See below. Dave C Are you interested in genomics and do you have skills in Bioinformatics, Computational Biology and Statistics? The Makova lab in the Department of Biology at The Pennsylvania State University is looking to hire a postdoctoral researcher for an NSF-funded project examining regional variation in mutation rates (see our recent publication in PNAS: Kuruppumullage Don, Ananda, Chiaromonte, Makova 2013)http://www.pnas.org//content/early/2013/08/16/1221792110.abstract. With new sequencing technologies, multiple human genomes and their detailed annotations (e.g., ENCODE) are suddenly accessible to us. This gives us a terrific opportunity to explore previously inaccessible evolutionary processes (e.g., mutation) and other biological associations (location of genes in certain mutation states, as identified by HMMs). Such knowledge is vital in a clinical setting where disease mutations need to be evaluated. Our resources and links with medical researchers at Hershey Medical School and computational biologists from the Galaxy teamhttp://galaxyproject.org/put us in a great position to address these questions. Candidates should have experience in bioinformatics, working knowledge of statistics and should have a broad understanding of molecular biology and genetics. Familiarity with next-generation sequencing data analysis is desirable. A PhD is required. You will be joining an established dynamic group. We are part of the Center for Medical Genomicshttp://www.huck.psu.edu/center/medical-genomicsand of the Center for Comparative Genomics and Bioinformatics http://www.bx.psu.edu/. Penn State is a vibrant scientific community with particular strengths in genomics, bioinformatics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent schools and numerous opportunities for outdoor activities. The starting date is flexible, with an earlier date preferred. This position is funded for one year from date of hire, with good possibility of refunding. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information for three referees to Kateryna Makova kmak...@bx.psu.edu, indicating postdoc in the subject line. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity, and the diversity of its workforce. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ZFS storage recommendations
Hi Joachim, Something that may help with benchmarking: At the July 2012 GalaxyAdmins meetup, Anne Black-Ziegelbein talked about how they evaluated filesystem options. She also included benchmarking scripts and data. See http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2012_07_09 Dave C On Tue, Sep 10, 2013 at 10:12 AM, Adam Brenner aebre...@uci.edu wrote: optimize performance? The purpose is to share the database over NFS to the Galaxy VM. Are you moving the PostgreSQL/MySQL database over to ZFS or the actual storage of your datasets over to ZFS? I am assuming the latter. Remember, ZFS is just a file system, you still need a protocol, like NFS, to export the data to each of your machines. This is going to be your bottleneck, luckily the NFS clients supports write caching as described in our test here[1]. On our HPC cluster, we run xfs filesystem on top of Gluster and we have another filesystem using xfs on top of FraunhoferFS. I did test out ZFS on Linux roughly a year ago and in terms of Read/Write on a single machine it was slower than native ext4 and XFS. This of course was to be expected. However the added benefit of ZFS may be more favorable in your case, Snapshots, disk management, ZIL/SSD caching, etc. If you use a distributed filesystem like Gluster, FraunhoferFS, or even Lustre (2.x branch supports ZFS!) you will most certainly get some very good read/write speeds. However, it sounds like you are using a single machine, so your read/write is going to be slower than native ext4 and XFS --- trust but verify, run your own read/write tests. When I was using ZFS, this ZFSBuild[2] website was most helpful. Let me know if you have any other questions, -Adam [1]: http://www.gluster.org/pipermail/gluster-users/2012-September/034295.html [2]: http://www.zfsbuild.com/ -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Tue, Sep 10, 2013 at 3:29 AM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi all, I am performing some tests to move my galaxy database to ZFS. Does anybody have experience with ZFS on linux, and some recommendations/experiences to optimize performance? The purpose is to share the database over NFS to the Galaxy VM. Thanks, Joachim. -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] August 2013 Galaxy Update Newsletter is out
Hello all, The September 2013 Galaxy Update is hot off the presshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09: - A record *five new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#New_Public_Servers * - 30 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#New_Papers - Take the 2014 Galaxy Training Surveyhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#A2014_Galaxy_Training_Survey - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Who.27s_Hiringat six different organizations - Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Eventsincluding training in California, Sydney, Italy, Toulouse, and Boston. - Aug 12, 2013 Galaxy Distributionhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Aug_12.2C_2013_Galaxy_Distribution - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Other_News If you have anything you would like to see in the next *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy Release Cycle Length
Hello all, At one of the GCC2013 Birds of a Feather sessionshttp://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers the group was very clear that they would like to see less frequent releases of Galaxy. We're currently aiming to do a release every 2 months and have been pretty successful at making that target. In the past, we have tried doing releases more often and less often. Is there a sweet spot for the time between releases? Please reply to the group. We are interested in a discussion. Thanks, Dave C -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] August 2013 Galaxy Update Newsletter is out
Hi Samuel, On Wed, Aug 7, 2013 at 8:04 AM, Samuel Lampa samuel.la...@gmail.com wrote: Thanks for the update, Dave! Was delighted to see that the videos from all the talks (except lightning talks) are up at: http://wiki.galaxyproject.org/**Events/GCC2013/Programhttp://wiki.galaxyproject.org/Events/GCC2013/Program And I am personally very impressed with the quality of those videos. I wanted to ask though, are there specific reasons for not using a service like YouTube / Vimeo etc? Yes! Um, but I can't remember what they are (sadly, this is true). We'll talk about this on the next outreach call, and I'll post here what we decide. And unlike what I said in the email, the Galaxy community has a new *Proteomics *mailing listhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Galaxy_Proteomics_Mailing_List . Thanks, Dave C That would make sharing on Google+ / Twitter / Facebook etc much nicer, since you get a preview and an in-page embedded player, (possibly) enabled commenting etc, which I think would help spread the word about Galaxy even more. Just my 5c, and big thanks for the hard work with putting all this up! (I know it is a tremendous lot of work) Best Regards // Samuel On 07/31/2013 07:51 PM, Dave Clements wrote: Hello all, The August 2013 Galaxy Update is now available http://wiki.galaxyproject.**org/GalaxyUpdates/2013_08http://wiki.galaxyproject.org/GalaxyUpdates/2013_08 . -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 2014 Galaxy Training Survey
Hello all, The Galaxy Project is asking for your help on how we should focus our training efforts for the coming year. If you are interested in Galaxy Training, please take a few minutes to let us know what you would like to see offered, and where you would like training to be held: http://bit.ly/gxy14training Thanks in advance for your time and input, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] August 2013 Galaxy Update Newsletter is out
Hello all, The August 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08 . *Highlights:* - *GCC2013 Reporthttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#GCC2013_Report :* Meeting summaries, and links to videos, talks, posters, and Training Day materials. - Two new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Public_Servers - 47 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Papers - SlipStream: Galaxy is now available as an appliancehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#SlipStream_Appliance:_Galaxy_Edition_Announced - There's a new Galaxy-Ptotoemics mailing listhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#New_Galaxy_Proteomics_Mailing_List - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Who.27s_Hiring at eight different organizations - Galaxy @ ISMBhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#ISMB_.2F_ECCB_.2F_BOSC_.2F_MS_SIG_2013: links to slides and posters - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Other_Upcoming_Events including training in California, Sydney, Italy, Toulouse, and Boston. - New CloudMan Releasehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#CloudMan_Release - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_08#Other_News If you have anything you would like to see in the next *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] (no subject)
Hello all, The July 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07 . *Highlights:* - *GCC2013 http://wiki.galaxyproject.org/Events/GCC2013* starts *today*in Oslo, Norway. - Four new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#New_Public_Servers - A record 53 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Who.27s_Hiring at five different organizations - Galaxy @ ISMBhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#ISMB_.2F_ECCB_.2F_BOSC_.2F_MS_SIG_2013 - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Other_Upcoming_Events - New distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Other_News If you have anything you would like to see in the August *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2013 Regular Registration closes June 14
Hello all, This is a reminder that registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Registerfor the 2013 Galaxy Community Conference (GCC2013http://wiki.galaxyproject.org/Events/GCC2013) closes June 14*, just ten days from today. *Registering nowhttp://wiki.galaxyproject.org/Events/GCC2013/Registeravoids the 100% late registration surcharges, and guarantees you a spot in the Training Day sessionshttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDayyou want to take. *Registration is still a bargain with the full 3-day registration starting at ~ €165 for post-docs and students (that is just €55 per day). The program http://wiki.galaxyproject.org/Events/GCC2013/Program features 15 Training Day sessionshttp://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C_30_June in 5 tracks on 12 different topics, 25 Talkshttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts on topics ranging from Reproducibilityhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FTalks.A1_July:_Session_1:_Reproducible_science to Exploiting Galaxyhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FTalks.A2_July:_Session_7:_Exploiting_Galaxy , 23 Postershttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Poster_Abstracts (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. GCC2013 is a great opportunity to share best practices from and network with other researchers also facing the challenges of data-intensive biology. Ser frem til å se deg i Oslo! GCC2013 Organizing Committee PS: and please help get the word outhttp://wiki.galaxyproject.org/Events/GCC2013/Promotion . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Information for Galaxy Event Horizon
Hi Sarah, We'd be happy to put this on the Galaxy Event Horizon page on the wiki. Since the event is over, we would list it in the past events section. Is there a web page for the workshop or slides that we can link to? And, for future reference, wiki update requests can be sent directly to Galaxy Outreach outre...@galaxyproject.org. Thanks, Dave C. On Thu, May 30, 2013 at 7:18 AM, Sarah Maman sarah.ma...@toulouse.inra.frwrote: ** Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/). This session is composed of four training days: - Galaxy first step - Reads alignment and SNP calling - RNAseq alignment and transcripts assemblies - sRNAseq Do you think it is possible to list our training session in your Galaxy Event Horizon? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAEhttp://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] June 2013 Galaxy Update
Hello all, The June 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06 . *Highlights:* - *Register http://wiki.galaxyproject.org/Events/GCC2013/Register for GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_06#GCC2013 by 7 June to avoid late registration rates* - Two new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#New_Public_Servers ODoSE and CBiB - 39 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#Who.27s_Hiring at four different institutions - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#Other_Upcoming_Events - Duplicate Accounts on Mainhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#Duplicate_Accounts_on_Main - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_06#Other_News If you have anything you would like to see in the July *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Next GalaxyAdmins Meetup: May 15; Galaxy @ Pathogen Portal
Hello all, Just a reminder that this is happening tomorrow, Wednesday, May 15. If you haven't taken a look at the Pathogen Portal Galaxy Server (*RNA-Rocket*, http://rnaseq.pathogenportal.org/) yet, please do. If you will be on the call, please connect a few minutes early, as it will take that long to get setup. Thanks, Dave C. On Wed, May 8, 2013 at 11:23 AM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, The next meetinghttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15 of the GalaxyAdmins Grouphttp://wiki.galaxyproject.org/Community/GalaxyAdmins will be held on May 15, 2013, at 10 AM Central US timehttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15 . Andrew Warren of the Cyberinfrastructure Divisionhttp://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division of the Virginia Bioinformatics Institute https://www.vbi.vt.edu/ at Virginia Tech will talk about their Galaxy deploymenthttp://rnaseq.pathogenportal.org/ at Pathogen Portal http://pathogenportal.org/, a highly customized Galaxy installation, and also about the group's objectives and future plans. Dannon Baker http://wiki.galaxyproject.org/DannonBaker will bring the group up to speed on what's happening in the Galaxy project. Date May 15, 2013 Time 10 am Central US Time (-5 GMT) Presentations *Galaxy http://rnaseq.pathogenportal.org/ at Pathogen Portalhttp://pathogenportal.org/ * Andrew Warren, Virginia Bioinformatics Institute https://www.vbi.vt.edu/, Virginia Tech *Galaxy Project Update* Dannon Baker http://wiki.galaxyproject.org/DannonBaker Links Meetup Linkhttps://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262346908659 Add to calendarhttps://globalcampus.uiowa.edu/build_calendar.event?meetingId=1262346908659 We use the Blackboard Collaborate Web Conferencing systemhttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/WebinarTech for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended. GalaxyAdmins http://wiki.galaxyproject.org/Community/GalaxyAdmins is a discussion group for Galaxy community members who are responsible for large Galaxy installations. Thanks, Dave Clements -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Next GalaxyAdmins Meetup: May 15; Galaxy @ Pathogen Portal
Hello all, The next meetinghttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15 of the GalaxyAdmins Grouphttp://wiki.galaxyproject.org/Community/GalaxyAdmins will be held on May 15, 2013, at 10 AM Central US timehttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15 . Andrew Warren of the Cyberinfrastructure Divisionhttp://www.vbi.vt.edu/faculty/group_overview/Cyberinfrastructure_Division of the Virginia Bioinformatics Institute https://www.vbi.vt.edu/ at Virginia Tech will talk about their Galaxy deploymenthttp://rnaseq.pathogenportal.org/ at Pathogen Portal http://pathogenportal.org/, a highly customized Galaxy installation, and also about the group's objectives and future plans. Dannon Baker http://wiki.galaxyproject.org/DannonBaker will bring the group up to speed on what's happening in the Galaxy project. Date May 15, 2013 Time 10 am Central US Time (-5 GMT) Presentations *Galaxy http://rnaseq.pathogenportal.org/ at Pathogen Portalhttp://pathogenportal.org/ * Andrew Warren, Virginia Bioinformatics Institute https://www.vbi.vt.edu/, Virginia Tech *Galaxy Project Update* Dannon Baker http://wiki.galaxyproject.org/DannonBaker Links Meetup Linkhttps://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262346908659 Add to calendarhttps://globalcampus.uiowa.edu/build_calendar.event?meetingId=1262346908659 We use the Blackboard Collaborate Web Conferencing systemhttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/WebinarTech for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended. GalaxyAdmins http://wiki.galaxyproject.org/Community/GalaxyAdmins is a discussion group for Galaxy community members who are responsible for large Galaxy installations. Thanks, Dave Clements -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] May 2013 Galaxy Update
Hello all, The May 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05 . *Highlights:* - the GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_05#GCC2013 *early registration deadline is 24 Mayhttp://wiki.galaxyproject.org/Events/GCC2013/Register *. - 39 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#Who.27s_Hiring at five different institutions - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#Other_Upcoming_Events - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_05#Other_News If you have anything you would like to see in the June *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GalaxyAdmins Group: Future Directions?
Hello all, Just some minor updates to refresh this thread. Most of this will be described in more detail in separate emails over the next two weeks. First, the next web meetup will be May 15. We haven't nailed down a main speaker yet, but Dannon Baker will be giving the project update. Second, I've created a Birds-of-a-Feather (BoF) session at GCC2013 to continue, and maybe just finish, this discussion in person at the meeting (see http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins). If you are interested in participating in that BoF, either send me an email, or add your name to that wiki page. (We will officially announce GCC2013 BoFs in a few weeks - after the poster abstract deadline, but feel free to get a head start and add your own now. :-) Third, should we start a separate email list for GalaxyAdmins business? It would have far fewer members and have far less traffic than Galaxy-Dev. I'm in favor of it. If you have an opinion, please post here. Thanks, Dave C On Wed, Apr 10, 2013 at 1:32 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, First, thanks to Srinivas and Hans for the responses. I have kept track of the head counts for most meetups: 2012/07/07 27 2012/07/27 ? (in person meetup at GCC2012) 2012/09/19 10 2012/11/07 17 2013/01/16 14 2013/03/20 15 So, maybe converging on mid-teens? This number is not as high as I had hoped. Srinivas, is there any way to tell how many times the screencasts have been watched afterword? I'm see the group as complimentary to Galaxy-Dev, and I am leaning towards creating a Galaxy-Admins maling list that is purely about the group and group activities (Ann BZ's idea originally). It would not be a support channel and any stray support postings would get redirected to Galaxy-Dev (or Galaxy-User, if that's where they belong). We would still post activities to Galaxy-Dev as well, but any group business (like this discussion) would happen only on Galaxy-Admins. On the group leadership issue I very much want the group to be led by people that are not part of the core team. I am quite willing to continue to fill the supportive role I've been doing for the past year. If GalaxyAdmins is to become a voice for the community at some point in the future, it should very definitely not be led by the core team. However, if our future consists only of bi-monthly meetups (which have been great!) then it does not matter as much. My 2p, Dave C On Tue, Apr 9, 2013 at 4:58 PM, Maddhi, Srinivas srinivas-mad...@uiowa.edu wrote: Hi Hans, Thanks for the response. I didn't mean to advocate for an overlapping group but rather to identify means to strengthen the existing dev and user group interactions. There might, however, be some value in evaluating whether we are at a point, in terms of number of deployment and support models for the same, wherein a Galaxy admin specific group or mailing list would make sense. We have had an estimated six to ten participants at the meet-ups that have occurred since September 2012. Best regards, Srinivas. -Original Message- From: Hans-Rudolf Hotz h...@fmi.ch Date: Monday, April 8, 2013 3:21 AM To: Srinivas Maddhi srinivas-mad...@uiowa.edu, Dave Clements cleme...@galaxyproject.org Cc: Galaxy Dev List galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hi Srinivas Thank you very much for e-mail...and thereby reminding me that I haven't replied to Dave's call a week ago. I second most of your thoughts. However, I am not sure of the idea of creating a full-fledged user group with additional opportunities for sharing, learning and collaborating. I like it, but how do you intend to distinguish this group from the current '[galaxy-dev]' group/community? I am afraid stuff will get lost between the two groups or it leads to duplication.probably something we need to discuss in Oslo? I am definitively in favor of a dual leadership - one person from the admin community and one from the Galaxy team. Regards, Hans-Rudolf PS: Do you have stats of who (or how many) has taken part in the past meetups? I think the numbers have been much smaller than the number of responses to Ann's original proposal last April. On 04/05/2013 10:43 PM, Maddhi, Srinivas wrote: Hello, Based on my observations and interactions during the past few meet-ups and as an administrator of Galaxy, the current goals of the group [1] remain relevant and are being met through the meet-ups. An additional benefit to these meet-ups that has evolved is an update from a member of the Galaxy team on upcoming features and other developments. With regard to the future of the group, my suggestion is to keep it going and work towards building a full-fledged user group with additional opportunities for sharing, learning and collaborating. This will strengthen the community
Re: [galaxy-dev] Teaching using Galaxy
Hi David, Using Galaxy to teach undergraduates is a long term interest of mine. Which, unfortunately, does not mean I have yet put a lot of thought into it. However, lack of thought hasn't stopped me yet. First, this topic was discussed in a breakout at last year's GCC: http://wiki.galaxyproject.org/Events/GCC2012/Program/Breakouts/BioinformaticsTraining That's more of a discussion than a set of best practices. What do you want them to spend time learning? Do you want them to learn the (sometimes grinding) details of using the command line, and how to install software and their dependencies on a Linux box? Or do you want to focus mainly on the high level stuff like here is how and why BLAST works, and get some practice using it? I think this question of focus is a central one, and it's one that well-informed people disagree on. Galaxy is a great platform for focussing on the high-level stuff and avoiding the frustration that can come with installing a C compiler, for example. On the other hand, if you really want them to learn the command line, then you might want to start elsewhere. If you do use Galaxy for teaching, there are a couple of ways you could do it. First, I recommend setting up your own server(s) either locally or on the cloud. (The AWS in Education grant program is built just for this case.) If you wanted to teach them a mixture of high-level and low level, you could start them out as users on a shared server, and then later in the course have them setup their own Galaxy on a cloud instance. Also, for Galaxy training we find that published histories, workflows, and Galaxy Pages, are a superb way to create exercises. Hope this helps, Dave C. On Mon, Apr 22, 2013 at 12:30 PM, David Joly idj...@gmail.com wrote: Hi everybody! I am currently creating a bioinformatics course for undergraduate (biology students with no knowledge of programming). I would like to use Galaxy as their everyday platform where they would learn the basics and use the appropriate tools (BLAST and databases, multiple alignment, phylogenetics, dealing with omics data, and so on). Is there any available resources about using Galaxy for teaching (undergraduates)? Any suggestions of good textbooks? Not a Galaxy textbook of course, but a bioinformatics textbook that would be a good companion to help the students understand the basics behind the tools. Thanks, DJ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Teaching using Galaxy
Hi David, Galaxy does sound like a great match for this course. It could also play a (smaller) part in the other course you are considering. Part of the course could include installing Galaxy and wrapping other tools to put into it. We are a Python based framework I do strongly recommend you look at http://aws.amazon.com/grants/ for both courses. We have been using Amazon in our workshops for a year now and it has been a big win. There is also a wealth of material out there on how other people train using Galaxy. See http://wiki.galaxyproject.org/Events#Past_Events - lots of links to presentations http://wiki.galaxyproject.org/Documents/Presentations - same material, different order http://wiki.galaxyproject.org/Learn - the Galaxy learning hub, especially http://wiki.galaxyproject.org/Learn#Other_Tutorials And, maybe, hopefully, real soon now, there will be a Galaxy Teaching and Training hub page as well (been on my TODO list for a while, but expect something before GCC2013, really). Dave C. On Wed, Apr 24, 2013 at 3:52 PM, David Joly idj...@gmail.com wrote: Thanks Dave! The focus is clearly more like your second description. The course is not intended to show them how to use command lines, or how to navigate in a UNIX environment and how to program. In fact, I think some would call what I have in mind more of a computational biology course than a bioinformatics course, but I think it is not really important here. I'm thinking of another course to introduce them to the UNIX environment and using Python to script simple programs, but for this one, I'd prefer staying away from a terminal that can be horrifying at first (for most students, black screen = evil) So, the course is about knowing the tools and their basics, and how to use them (in this case using Galaxy as the platform). What is a sequence alignment, why should we do a sequence alignment, how a sequence alignment work, and how can I do one in Galaxy. This is only one example, other (and often inter-related) topics would include BLAST, phylogenetics, sequence polymorphisms, and so on, up to analyzing next-generation sequencing data... Regarding how I'll set my environment, I was thinking of setting a local instance (I have one on my computer right now and I'm already getting familiar with it). The hardware on which I'll set the instance for the course is another issue, but this is not the topic of this email... I'll have a better look at how I could use published histories and workflows... Thanks, DJ 2013/4/24 Dave Clements cleme...@galaxyproject.org Hi David, Using Galaxy to teach undergraduates is a long term interest of mine. Which, unfortunately, does not mean I have yet put a lot of thought into it. However, lack of thought hasn't stopped me yet. First, this topic was discussed in a breakout at last year's GCC: http://wiki.galaxyproject.org/Events/GCC2012/Program/Breakouts/BioinformaticsTraining That's more of a discussion than a set of best practices. What do you want them to spend time learning? Do you want them to learn the (sometimes grinding) details of using the command line, and how to install software and their dependencies on a Linux box? Or do you want to focus mainly on the high level stuff like here is how and why BLAST works, and get some practice using it? I think this question of focus is a central one, and it's one that well-informed people disagree on. Galaxy is a great platform for focussing on the high-level stuff and avoiding the frustration that can come with installing a C compiler, for example. On the other hand, if you really want them to learn the command line, then you might want to start elsewhere. If you do use Galaxy for teaching, there are a couple of ways you could do it. First, I recommend setting up your own server(s) either locally or on the cloud. (The AWS in Education grant program is built just for this case.) If you wanted to teach them a mixture of high-level and low level, you could start them out as users on a shared server, and then later in the course have them setup their own Galaxy on a cloud instance. Also, for Galaxy training we find that published histories, workflows, and Galaxy Pages, are a superb way to create exercises. Hope this helps, Dave C. On Mon, Apr 22, 2013 at 12:30 PM, David Joly idj...@gmail.com wrote: Hi everybody! I am currently creating a bioinformatics course for undergraduate (biology students with no knowledge of programming). I would like to use Galaxy as their everyday platform where they would learn the basics and use the appropriate tools (BLAST and databases, multiple alignment, phylogenetics, dealing with omics data, and so on). Is there any available resources about using Galaxy for teaching (undergraduates)? Any suggestions of good textbooks? Not a Galaxy textbook of course, but a bioinformatics textbook that would be a good companion to help
[galaxy-dev] Fwd: [Gmod-announce] 2013 GMOD Summer School: Apply now!
Hello all, The 2013 GMOD Summer School is now accepting applications. Galaxy will again be included in the topics covered. And Amelia says: Applications are competitive, so we encourage you to apply well before the deadline, June 10th. So, if you are interested, act soon. Dave C -- Forwarded message -- From: Amelia Ireland amelia.irel...@gmod.org Date: Wed, Apr 17, 2013 at 11:15 AM Subject: [Gmod-announce] 2013 GMOD Summer School: Apply now! To: gmod-announce gmod-annou...@lists.sourceforge.net, gmod-de...@lists.sourceforge.net We are now accepting applications for the 2013 GMOD Summer School, to be held NESCent, Durham, North Carolina from July 19th to 23rd. The GMOD Summer School is the best way to learn how to install, configure, and use popular GMOD tools, including GBrowse, JBrowse, Galaxy, MAKER, Tripal, WebApollo, and Chado; courses are taught by the tool developers, and there will be evening sessions for those who want to work on their own data or troubleshoot issues with the developers. More information and online application form: http://gmod.org/wiki/2013_GMOD_Summer_School Applications are competitive, so we encourage you to apply well before the deadline, June 10th. If you have any questions, please contact h...@gmod.org and we will be happy to answer them. -- Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ Gmod-announce mailing list gmod-annou...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-announce -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GalaxyAdmins Group: Future Directions?
Hello all, First, thanks to Srinivas and Hans for the responses. I have kept track of the head counts for most meetups: 2012/07/07 27 2012/07/27 ? (in person meetup at GCC2012) 2012/09/19 10 2012/11/07 17 2013/01/16 14 2013/03/20 15 So, maybe converging on mid-teens? This number is not as high as I had hoped. Srinivas, is there any way to tell how many times the screencasts have been watched afterword? I'm see the group as complimentary to Galaxy-Dev, and I am leaning towards creating a Galaxy-Admins maling list that is purely about the group and group activities (Ann BZ's idea originally). It would not be a support channel and any stray support postings would get redirected to Galaxy-Dev (or Galaxy-User, if that's where they belong). We would still post activities to Galaxy-Dev as well, but any group business (like this discussion) would happen only on Galaxy-Admins. On the group leadership issue I very much want the group to be led by people that are not part of the core team. I am quite willing to continue to fill the supportive role I've been doing for the past year. If GalaxyAdmins is to become a voice for the community at some point in the future, it should very definitely not be led by the core team. However, if our future consists only of bi-monthly meetups (which have been great!) then it does not matter as much. My 2p, Dave C On Tue, Apr 9, 2013 at 4:58 PM, Maddhi, Srinivas srinivas-mad...@uiowa.eduwrote: Hi Hans, Thanks for the response. I didn't mean to advocate for an overlapping group but rather to identify means to strengthen the existing dev and user group interactions. There might, however, be some value in evaluating whether we are at a point, in terms of number of deployment and support models for the same, wherein a Galaxy admin specific group or mailing list would make sense. We have had an estimated six to ten participants at the meet-ups that have occurred since September 2012. Best regards, Srinivas. -Original Message- From: Hans-Rudolf Hotz h...@fmi.ch Date: Monday, April 8, 2013 3:21 AM To: Srinivas Maddhi srinivas-mad...@uiowa.edu, Dave Clements cleme...@galaxyproject.org Cc: Galaxy Dev List galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hi Srinivas Thank you very much for e-mail...and thereby reminding me that I haven't replied to Dave's call a week ago. I second most of your thoughts. However, I am not sure of the idea of creating a full-fledged user group with additional opportunities for sharing, learning and collaborating. I like it, but how do you intend to distinguish this group from the current '[galaxy-dev]' group/community? I am afraid stuff will get lost between the two groups or it leads to duplication.probably something we need to discuss in Oslo? I am definitively in favor of a dual leadership - one person from the admin community and one from the Galaxy team. Regards, Hans-Rudolf PS: Do you have stats of who (or how many) has taken part in the past meetups? I think the numbers have been much smaller than the number of responses to Ann's original proposal last April. On 04/05/2013 10:43 PM, Maddhi, Srinivas wrote: Hello, Based on my observations and interactions during the past few meet-ups and as an administrator of Galaxy, the current goals of the group [1] remain relevant and are being met through the meet-ups. An additional benefit to these meet-ups that has evolved is an update from a member of the Galaxy team on upcoming features and other developments. With regard to the future of the group, my suggestion is to keep it going and work towards building a full-fledged user group with additional opportunities for sharing, learning and collaborating. This will strengthen the community, possibly drive increased adoption, and further serve to guide development of Galaxy. Appointing one of more leaders (one each from the Galaxy team and user community) to identify speakers, drive the agenda, set a cadence to the meet-ups and drive the formation of a user group would be helpful, IMHO. Thanks! Notes: 1. Build a community, learn from each other From: Dave Clements cleme...@galaxyproject.org mailto:cleme...@galaxyproject.org Date: Monday, April 1, 2013 11:07 AM To: Galaxy Dev List galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Subject: [galaxy-dev] GalaxyAdmins Group: Future Directions? Hello all, The GalaxyAdmins group is coming up on it's one year anniversary (coinciding with GCC2013) and this is a good opportunity to discuss what the future of the group should be. Some starting topics for discussion are on the GalaxyAdmins Future Directions page (http://wiki.galaxyproject.org/Community/GalaxyAdmins/Future). These include * What should the group's goals and activities be? * What type of leadership structure should
[galaxy-dev] GCC2013 Talk Abstract Submission closes this Friday
Hello all, This is a final reminder that the *deadline for submitting an oral presentation abstract is this 12 April, this Friday*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. And in case you missed the announcement about GIgaScience and GCC2013 talks: We are pleased to announce that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience http://www.gigasciencejournal.com/* and that BGIhttp://www.genomics.cn/en/indexwill generously cover the article processing fees for these articles. See the announcement http://wiki.galaxyproject.org/News/GigaScienceGalaxyCFPfor details. Thanks, Dave C On Mon, Feb 25, 2013 at 3:40 AM, Dave Clements cleme...@galaxyproject.orgwrote: Dear Galaxy Community, We are pleased to announce that early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register and paper and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open for the 2013 Galaxy Community Conference (GCC2013)http://wiki.galaxyproject.org/Events/GCC2013 . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo http://uio.no/. GCC2013 http://wiki.galaxyproject.org/Events/GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register * *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2013/Organizers PS: And please help get the word outhttp://wiki.galaxyproject.org/Events/GCC2013/Promotion ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Call for papers for a special GCC2013 and Galaxy series in GigaScience
Hello all, I am pleased to inform you that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience* and that BGI will generously cover the article processing fees for these articles. See the announcement below for details. thanks, Dave C The 2013 Galaxy Community Conference (GCC2013)http://wiki.galaxyproject.org/Events/GCC2013 and BioMed Central http://www.biomedcentral.com/ are announcing a special thematic series in *GigaScience http://www.gigasciencejournal.com/ *, a new journal co-published in collaboration between BGI Shenzhenhttp://www.genomics.cn/en/index and BioMed Central http://www.biomedcentral.com/ focused on studies utilizing large-scale datasets and workflows. Galaxyhttp://galaxyproject.org/ is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committeehttp://wiki.galaxyproject.org/Events/GCC2013/Organizers#Scientific_Committee, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing chargeshttp://www.gigasciencejournal.com/about/apcfaq for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiershttp://en.wikipedia.org/wiki/Digital_object_identifier from the journal's Giga-Galaxy server http://galaxy.cbiit.cuhk.edu.hk/ and GigaDB database http://gigadb.org/. Please contact the conference organizers gcc2013-...@galaxyproject.org or GigaScience editors editor...@gigasciencejournal.com for further information, or submit a manuscripthttp://www.gigasciencejournal.com/authors/instructions/research or conference abstracthttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open serieshttp://www.gigasciencejournal.com/series . Scott Edmunds Executive Editor *GigaScience http://www.gigasciencejournal.com/* -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GCC2013 Oral Presentation Abstract Submission Closes 12 April
Hello all, This is just a reminder that the *deadline for submitting an oral presentation abstract is 12 April, which is less than two weeks away*. See http://wiki.galaxyproject.org/Events/GCC2013/Abstracts The poster presentation abstract deadline is 3 May. Thanks, Dave C On Sun, Feb 24, 2013 at 7:40 PM, Dave Clements cleme...@galaxyproject.orgwrote: Dear Galaxy Community, We are pleased to announce that early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register and paper and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open for the 2013 Galaxy Community Conference (GCC2013)http://wiki.galaxyproject.org/Events/GCC2013 . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo http://uio.no/. GCC2013 http://wiki.galaxyproject.org/Events/GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register * *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2013/Organizers PS: And please help get the word outhttp://wiki.galaxyproject.org/Events/GCC2013/Promotion ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] GalaxyAdmins Group: Future Directions?
Hello all, The GalaxyAdmins group is coming up on it's one year anniversary (coinciding with GCC2013) and this is a good opportunity to discuss what the future of the group should be. Some starting topics for discussion are on the GalaxyAdmins Future Directions page (http://wiki.galaxyproject.org/Community/GalaxyAdmins/Future). These include * What should the group's goals and activities be? * What type of leadership structure should the group have, and how should it be selected? The discussion, however, is wide open to any topic relevant to the group. If you have any opinions or suggestions please reply to the group. Anyone with an interest in the group is encouraged to post. Once the discussion settles, I will summarize the discussion on the wiki page and suggest an action plan for making those things happen. Thanks, Dave C. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] April 2013 Galaxy Update
Hello all, The April 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04. (http://wiki.galaxyproject.org/GalaxyUpdates/2013_04) *Highlights:* - The GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_04#GCC2013 *oral presentation abstract deadline is 12 Aprilhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts *, which is less than 2 weeks away. Early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register, and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are also open. - Two new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#New_Public_Galaxy_Servers are featured - The slides and screencast for the March GalaxyAdmins meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#GalaxyAdmins are available. - And, please help determine what the GalaxyAdmins group should focus onhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#GalaxyAdmins_Future_Directions - 32 new papers and 5 new tagshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#Who.27s_Hiring at six different institutions - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#Other_Upcoming_Events - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_04#Other_News If you have anything you would like to see in the May *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cloudman on openstack
Hi Zeeshan, There has actually been quite a bit of work on supporting CloudMan on OpenStack. The whole NECTAR deployment in Australia is based on OpenStack. What there has not been, as far as I know, is documentation about it. I suggest creating a Trello card on this (see http://wiki.galaxyproject.org/Issues#Create_an_Issue). That will allow others to comment on it and up-vote it, which will make it get done sooner. Sorry not to be of more help right now. Dave C On Wed, Mar 20, 2013 at 1:24 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, any update for cloudman with openstack . the page seems quite old http://wiki.galaxyproject.org/CloudMan/OpenStack -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah ___ 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/ -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Search software on public Galaxy servers
Hi Bernardo, I'm intrigued by this idea. It might be possible to build a Google custom search, similar to the Tools tab of the usegalaxy search ( http://galaxyproject.org/search/usegalaxy/). That's would not be an ideal solution, but it would be quick to implement. Let me take a look at this in a week or two (traveling this week) and see if searching ~28 sites is tractable/possible with a free Google custom search. Thanks, Dave C On Thu, Feb 28, 2013 at 8:02 AM, Bernardo Bello popn...@gmail.com wrote: Hi community, Due to the increasing Galaxy public servers PublicGalaxyServershttp://wiki.galaxyproject.org/PublicGalaxyServers it would be very useful to have a search tool in order to look for software ready-to-use in the public servers. Since I know this is not available. Will it be feasible? Here is the Trello Card https://trello.com/c/FdF5h17c Regards, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona, Spain) Tel.: 647 42 52 63 *www.cresa.es * * * ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] March 2013 Galaxy Update
Hello all, The March 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03. See http://wiki.galaxyproject.org/GalaxyUpdates/2013_03. *Highlights include:* - *GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_03#GCC2013 early registration http://wiki.galaxyproject.org/Events/GCC2013/Register, and oral presentation and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open*, and we have several new sponsorshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Sponsorships ! - The March 20 GalaxyAdmins meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#March_GalaxyAdmins_Web_Meetup will feature Hailiang (Leon) Mei, and David van Enckevort speaking on *NBIC Galaxy http://galaxy.nbic.nl/ at SURFsara's HPC cloudhttps://www.surfsara.nl/ * - A new public Galaxy serverhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#New_Public_Galaxy_Servers in Costa Rica - New papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Who.27s_Hiring at four different institutions - Other Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Other_Upcoming_Events_and_Deadlines - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Other_News If you have anything you would like to see in the April *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave C -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] 2013 Galaxy Community Conference (GCC2013) Registration and Abstract Submission are Now Open
Dear Galaxy Community, We are pleased to announce that early registrationhttp://wiki.galaxyproject.org/Events/GCC2013/Register and paper and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open for the 2013 Galaxy Community Conference (GCC2013)http://wiki.galaxyproject.org/Events/GCC2013 . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo http://uio.no/. GCC2013 http://wiki.galaxyproject.org/Events/GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registration http://wiki.galaxyproject.org/Events/GCC2013/Register* *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Dayhttp://wiki.galaxyproject.org/Events/GCC2013/TrainingDay + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committeehttp://wiki.galaxyproject.org/Events/GCC2013/Organizers PS: And please help get the word outhttp://wiki.galaxyproject.org/Events/GCC2013/Promotion ! -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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 @ GMOD2013 Biocuration 2013
Hello all, There are a couple of things going on with the GMOD Projecthttp://gmod.org/wiki/ that the Galaxy Community might be interested in. If you aren't familiar with GMOD, it is a federation of open-source projects and tools that enable visualizing, annotating, managing, and analyzing biological research data. GMOD includes Galaxy and several other widely used tools such as BioMarthttp://gmod.org/wiki/BioMart , InterMine http://gmod.org/wiki/InterMine, MAKERhttp://gmod.org/wiki/MAKER , Chado http://gmod.org/wiki/Chado and GBrowsehttp://gmod.org/wiki/GBrowse and JBrowse http://gmod.org/wiki/JBrowse. The first is that GMOD is running a community-wide surveyhttp://gmod.org/survey.html through March 1. The survey aims to find out how you are using GMOD, what you find useful (or otherwise), what support you need, and some information on the GMOD components you use. The survey results will be published at gmod.organd past surveys have been extremely useful to the project. If that's not enough motivation, once you are done with the survey, you can enter to win a free genome profile from 23andMe. - → *C'mon, take the dang survey http://gmod.org/survey.html.* The second is that registration is now open for the 2013 GMOD Meetinghttp://gmod.org/wiki/April%202013%20GMOD%20Meeting being held in Cambridge, UK, April 5 and 6. There will be a Galaxy presence (at least a project update, and I'm lobbying for a CloudManhttp://wiki.galaxyproject.org/CloudMan workshop as well (and you could lobby too! h...@gmod.org)). Finally, Biocuration 2013 http://www.ebi.ac.uk/biocuration2013/home is immediately after the GMOD Meeting, and also in Cambridge. Biocuration will feature a GO Galaxy Workshophttp://wiki.geneontology.org/index.php/GO_Galaxy_Workshop_at_Biocuration_2013 about using Galaxy to reason with ontologies. Thanks, Dave Clements -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Fwd: Desire to contribute
Hi Matt, Here are a couple of things to consider: 1. Fix Select tool to match special characters: https://trello.com/c/cwrBpNP9 2. Extend history export to include composite dataset objects/files: https://trello.com/c/oq1ASbkC There are lots of other ideas, but they tend to be a lot more work. Please let the list know if any of the ideas posted so far grab you, or if you want further explanation. Thanks for your interest and for picking the Galaxy Project. Efforts like these really help the project move forward. Dave C On Tue, Feb 5, 2013 at 8:16 PM, Matthew Paul mrp...@g.cofc.edu wrote: Dear Galaxy Project community, I am working with a group of students at College of Charleston of South Carolina. Being interested in bioinformatics and software engineering, we chose to work on Galaxy for our open source class project. We are subscribed to the appropriate mailing list, have been accessing Trello and are becoming familiar with the Galaxy architecture. Our first assignment is to identify and fix a bug, but unfortunately the bugs reported seem to be going right over our heads.Where would be a good place to start, so that we may be able to contribute to your system (documentation, etc)? We are looking forward to your response. Thank you, Matt Paul -- Forwarded message -- From: Matthew Paul mrp...@g.cofc.edu Date: Tue, Feb 5, 2013 at 8:10 PM Subject: Desire to contribute To: galaxy-dev@lists.bx.psu.edu Dear Galaxy Project community, ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] February 2013 Galaxy Update
Hello all, The February 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02 at http://wiki.galaxyproject.org/GalaxyUpdates/2013_02 *Highlights:* - Three new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#New_Papers - New papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Who.27s_Hiring at five different institutions - GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_02#GCC2013 Training Day Topic voting, Registration, and Sponsorships - January GalaxyAdmins Web Meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#January_GalaxyAdmins_Web_Meetup slides and screencast - Other Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Other_Upcoming_Events_and_Deadlines - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#Other_News If you have anything you would like to see in the March *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave Clements http://wiki.galaxyproject.org/DaveClements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Wiki reset password's email never arrives
Hi Carlos, There does not appear to be an email address associated with your account. I will try to associate your account with your GMail account and let you know (off-list) when I think that is done. And, administrative requests like these can also be sent directly to outre...@galaxyproject.org, instead of to the list. However, the difference between wiki is broken is and administrative request is not always clear. Thanks, Dave C. On Wed, Jan 30, 2013 at 9:14 AM, Carlos Borroto carlos.borr...@gmail.comwrote: Hi, I need help recovering my Galaxy Wiki password. I enter my information and I get the message about my account existing and an email was sent, but I never receive this email. Thanks, Carlos ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Problem uploading to Galaxy
Hi Andrew, If this was on Main at Penn State, there was a problem with uploads that we believe has now been resolved. Dave C On Wed, Jan 16, 2013 at 5:21 PM, Andrew Gorzalski gorzal...@gmail.comwrote: Hello, I've encountered a problem uploading some .xlsx files to Galaxy. None of the files I've tried uploading today, via html or ftp, have been successfully uploaded. Instead, the box turns grey and says the Job is waiting to run. If I try to refresh, I get the error: The 'Upload File' tool does not currently support rerunning. Uploading the files to your ftp server and then using Get file gives the same result. Any help or suggestions? Andrew Gorzalski ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] login problems
Hi Eleanne, Take a look at http://wiki.galaxyproject.org/FTPUpload. FTP also needs to be enabled on the Galaxy server you are using. Which server are you trying to connect to? Thanks, Dave C. On Fri, Jan 18, 2013 at 10:42 AM, Solorzano, Eleanne eleanne.solorz...@unh.edu wrote: Hello, I am trying to connect to ftp with my username and password that I registered in galaxy. I am doing this through Filezilla. I am getting the error could not connect to server. Do you know what the problem is, please? Thank you. Eleanne ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] December 2012 Galaxy Update
Hello all, The December 2012 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12at http://wiki.galaxyproject.org/GalaxyUpdates/2012_12. *Highlights:* - 37 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Papers, including papers on Trackster and CloudMan - Two new public Galaxy Servershttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Public_Galaxy_Servers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Who.27s_Hiringat seven different institutions - Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Upcoming_Events_and_Deadlines - Source Code Documentationhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Source_Code_Documentationis now available - New Galaxy Distributionhttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_Distributions - New Galaxy CloudMan Releasehttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#New_Galaxy_CloudMan_Release - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2012_12#Other_News If you have anything you would like to see in the January *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Is there any timeout in Galaxy
Hi Akshay, I don't know the answer to your question. So: 1) I went to http://galaxyproject.org/search/web/ and searched for timeout and then timeout workflow. There are lots of email threads (and I learned some stuff :-), but I didn't find a direct answer to your question. 2) I'm sending your question to the galaxy-dev list where it will be seen by hundreds of galaxy admins and tool developers. (And this thread will also be found by any future searches.) Thanks, Dave C On Thu, Nov 15, 2012 at 8:33 AM, akshaycho...@gmail.com wrote: Hello, My name is Akshay and I am a computer science graduate student at UGA in Dr. Kissinger's Lab. We have created an extension to galaxy which allowed users to add web services as tools into galaxy, these could be either used as stand-alone or in a workflow. I wanted to know if Galaxy employs any time out strategy. Consider a case where I have a workflow with BLASTP now it takes some time to run blast and then get result form it. When I try that experiment as standalone (i.e., running the run method first and then after several mins getting result using job id works) however when I create a workflow in which one tool being run method of blast followed by getresult, galaxy seems to time out. Would appreciate your feedback on the same. -Akshay Choche Graduate Research Assistant (Kissinger Research Group) Center for Tropical and Emerging Global Diseases The University of Georgia, Athens, GA - 30605 Tele: 256-520-6541 Email: acho...@uga.edu, akshaycho...@gmail.com http://www.cs.uga.edu/~choche -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] [galaxy-announce] GalaxyAdmins meeting -- Nov 14 at 10 AM Central
Hello all, Just a reminder that the November GalaxyAdmins web meetup is tomorrow, Wednesday, at 10 am central US time. Details are below. Please join us, Dave C On Mon, Nov 5, 2012 at 3:28 PM, IIHG Galaxy Administrator iihg-galaxy-ad...@uiowa.edu wrote: Hello, The next meeting of the GalaxyAdmins group will be held on November 14 at 10 AM Central time. Curtis Hendrickson of the University of Alabama Birmingham's Center for Clinical and Translational Science (UAB CCTS) will speak on Deploying Galaxy on a shared-node cluster at UAB. The meeting will also include time for open discussion. Your active participation is encouraged. Thank you! Notes: - Link to the webinar: https://globalcampus.uiowa.edu:443/join_meeting.html?meetingId=1262339408056https://globalcampus.uiowa.edu/join_meeting.html?meetingId=1262339408056 - Meeting invite is attached - This information is also posted at http://wiki.galaxyproject.org/News/2012_11GalaxyAdmins -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics The University of Iowa ___ galaxy-announce mailing list galaxy-annou...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-announce To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Galaxy at Duke
Hi Alan, I'm CC'ing the Galaxy-Dev list on my response to your question. I talked with Jen Jackson on this. Her suggestion is that the symlink is most likely the problem somehow - this time. When in doubt, getting rid of these good place to start. So recommended starting solution to try - use full paths for everything. Also probably keep all on same partition for the best performance, but that would be hard to defend (there was some debate about this recently). Many thanks to Jen for her (as always) careful consideration. Dave C. On Mon, Nov 5, 2012 at 7:15 AM, Alan V. Cowles alan.cow...@duke.edu wrote: Hey Dave, Thanks for getting back in touch with me. We are running our galaxy instance on a vm... with Centos (RHEL) 6.2, 2 vcpus, and 2gb vram, with a remote postgresql prod server as our database instance. Our first issue was trying to get it so we could load sequence and larger files directly from an nfs mounted directory on the server, without uploading via the web (php vs large files problem.) We accomplished this via the data libraries interface but it's still not very user intuitive. Our first demo user attempted to upload 3 large files and actually filled up the / partition on the server as galaxy was installed at /usr/local. After scrapping and rebuilding that, we now have a several hundred GB nfs partition, mounted and /usr/local/galaxy is a symlink to a folder on this volume. The issue we are currently seeing is during an upload, or even just linking files it runs for a while before erroring out and saying there is no information on the error. The file seems to be there and taking up the correct amount of disk space but galaxy has a red bar. The galaxy server instance is running back grounded in a screen so we can always switch over and look at the output it shows to standard out as errors happen, and it seems that it has trouble changing permissions on the files in the nfs directory, even though, root squash is disabled, and the entire directory is 777 at the top level and everything underneath is owned galaxy:galaxy. AC -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] October 2012 Galaxy Update
Hello all, The October 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10 :** - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#Upcoming_Events_and_Deadlines - 35 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#New_Papers - CBIIT's new public Galaxy Serverhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#New_Public_Server:_CBIIT - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#Who.27s_Hiringat three different institutions - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#Tool_Shed_Contributions - New Distributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#New_Distributionss - Other News http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_10#Other_News If you have anything you would like to see in the November *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] September 2012 Galaxy Update
Hello all, The September 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09. *Highlights:* - 41 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Papers(a new monthly high) - 3 new public Galaxy Servershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Public_Servers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Who.27s_Hiringat four different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Upcoming_Events_and_Deadlines - Swiss Galaxy Day is October 3!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Swiss_Galaxy_Day - New Galaxy-France mailing listhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#New_Galaxy-France_Mailing_List - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Tool_Shed_Contributions - Other News http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09#Other_News If you have anything you would like to see in the October *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave Clements -- http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_09 http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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-France -- Communauté française de Galaxy (French Galaxy Community)
Bonjour à tous, Avec l'aide et le soutien de l'équipe Galaxy, nous venons de mettre en ligne la liste de diffusion Galaxy France. Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français. Vous avez besoin d'aide dans l'utilisation de Galaxy, Vous hébergez un serveur public Galaxy, Vous maintenez une instance locale de Galaxy, Vous venez de déposer un outil sur le toolshed, Vous avez des trucs et astuces pouvant interresser la communauté, Vous organisez des formations avec Galaxy, Rejoignez nous en vous inscrivant à http://lists.bx.psu.edu/listinfo/galaxy-france Les archives de cette liste sont disponibles à http://france.list.galaxyproject.org A très bientôt sur la liste Galaxy France, Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements Jennifer Jackson -- - Hi everyone, With the help and the support of the Galaxy team, we just put online the Galaxy French mailing list. The aim of this list is to share and communicate on our different experiences with Galaxy in France. * The main language is French. * Topics include, but are not limited to: You need help in the use of Galaxy, You're hosting a Galaxy public server, You're maintaining a local instance of Galaxy, You just add a new tool on the toolshed, You have some tips that could interested the community, You organize workshops with Galaxy, Join us by subscribing at http://lists.bx.psu.edu/listinfo/galaxy-france The list's archives are also available at http://france.list.galaxyproject.org See you soon on the Galaxy-France list, The administrators: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements Jennifer Jackson -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] August 2012 Galaxy Update
Hello all The August 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08at http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08. Highlights include - GCC2012 GCC2013http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#GCC2012_.26_GCC2013: slides are there; video is coming - Other Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Upcoming_Events_and_Deadlines - Swiss Galaxy Dayhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Swiss_Galaxy_Day - 29 new papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Who.27s_Hiringat four different institutions - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Tool_Shed_Contributions - New Distributionhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#New_Distributions - Other News http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_08#Other_News If you have anything you would like to see in the September *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks Dave Clements -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] July 2012 Galaxy Update
Hello all, The July 2012 Galaxy Update is now availablehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07. *Highlights:* - GCC2012 is July 25-27!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#GCC2012_is_July_25-27.21 - Register by July 18http://wiki.g2.bx.psu.edu/Events/GCC2012/Register - Other Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Upcoming_Events_and_Deadlines ,* including these deadlines in the next several days* - Galaxy Workshops in South Africahttp://wiki.g2.bx.psu.edu/News/GalaxyWorkshopsInSouthAfrica(deadline: *June 30*) and the South African Genetics Bioinformatics Society Conference http://genetics.cmc-uct.co.za/ (deadline *July 1*) - Systems Bioinformatics Workshophttp://gaggle.systemsbiology.net/workshop2012/(deadline: *June 30*) - GMOD Summer Schoolhttp://gmod.org/wiki/2012%20GMOD%20Summer%20School(deadline: *July 9*) - 31 New Papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Papers, including two new *Current Protocols* - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Who.27s_Hiringat six different institutions - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Tool_Shed_Contributions - A new CloudMan distribution was released last monthhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Distributions - Plus http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Other_News - Easily wrap your R functions as Galaxy tools - help schedule the first GalaxyCzarshttp://wiki.g2.bx.psu.edu/Community/GalaxyCzarsconference call on July 9 or 10 - and lots of new screencasts, tutorials, and new genomes on main If you have anything you would like to see in the August *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] GCC2012 Early Registration ENDS THIS MONDAY JUNE 11
Hello all, Just a *final* reminder that early registration for the 2012 Galaxy Community Conference (GCC2012)http://galaxyproject.org/wiki/Events/GCC2012 *closes on Monday June 11 (*which is probably* today* when you read this*)*. Registering early saves 36 to 42% on registration costs, and allows you to sign up for the GCC2012 Training Dayhttp://galaxyproject.org/wiki/Events/GCC2012/TrainingDayand book discounted conference lodginghttp://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging *before they fill up*. *Register today http://wiki.g2.bx.psu.edu/Events/GCC2012/Register. * GCC2012 http://galaxyproject.org/wiki/Events/GCC2012 will be held July 25-27, in Chicago, Illinois, United States. This year GCC2012 features a full day of tutorial sessionshttp://galaxyproject.org/wiki/Events/GCC2012/TrainingDaywith 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topic, including the newly added Variant and SNP Analsys, RNA-Seq Analysis, and Galaxy Code Architecture sessionshttp://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay. The two-day main meetinghttp://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Day_1:_July_26.2C_Thursdayincludes over 25 talks by Galaxy community members and Galaxy developers addressing the challenges of integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy http://gmod.org/wiki/Galaxyis an open web-based platform for data intensive biomedical researchhttp://galaxyproject.orgthat is widely used and deployed at research organizations of all sizes around the world. See you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committeehttp://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] GCC2012 Early Registration ends in 1 week
Hello all, Just a reminder that early registration for the 2012 Galaxy Community Conference (GCC2012) http://galaxyproject.org/wiki/Events/GCC2012, being held in Chicago, Illinois, July 25-27, *closes on June 11, one week from today*. Registering early saves 36 to 42% on registration costs, and allows you to book discounted conference lodginghttp://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging *before it fills up*. Register nowhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Register . GCC2012 http://galaxyproject.org/wiki/Events/GCC2012 is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. This is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy http://gmod.org/wiki/Galaxy is an open web-based platform for data intensive biomedical research http://galaxyproject.org that is widely used and deployed at research organizations of all sizes and around the world. The GCC2012 Training Dayhttp://galaxyproject.org/wiki/Events/GCC2012/TrainingDayagenda has been finalized. It has 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topics. The final schedulehttp://wiki.g2.bx.psu.edu/Events/GCC2012/Programof speakershttp://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakersand abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts are also now available. Hope to see you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committeehttp://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] June 2012 Galaxy Update
Hello all, The June 2012 Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06is now available. *Highlights:* - GCC2012 is Next Month!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#GCC2012_is_Next_Month.21 - *Early registration ends June 11http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#GCC2012_is_Next_Month * - New Public Server: GWIPS-Vizhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Public_Server:_GWIPS-Viz - 32 New Papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Who.27s_Hiringat six different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Upcoming_Events_and_Deadlines - *Early registration for ISMB/BOSC/BSI-SIG ends todayhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Upcoming_Events_and_Deadlines * - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Tool_Shed_Contributions - A new distribution was released last monthhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Distribution - GalaxyCzars survey results are inhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Other_News If you have anything you would like to see in the July *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave Clements -- *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complement the *Galaxy Development News Briefshttp://wiki.g2.bx.psu.edu/DevNewsBriefs * which accompany new Galaxy releases and focus on Galaxy code updates. http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Integrating Galaxy with JIRA for auto-ticket opening upon report
Hi Ann, This code has been to added to the queue of items to be folded into the main release. A developer will be in touch if and when they have questions. Thanks for submitting this. Dave C. On Wed, May 23, 2012 at 9:14 AM, Ann Black-Ziegelbein annbl...@eng.uiowa.edu wrote: Hi - We have integrated our local galaxy with JIRA such that when problems are reported through the galaxy interface, a problem ticket is automatically opened up. I had to make very minor changes to Galaxy in support of this, and I am contributing back my changes in this email in hopes they can be integrated in. What I changed: 1) config.py - support of a new config parm : error_email_from 2) dataset.py report_error - to use the new from email address if specified. 3) added in the new config parm to my universe_wsgi.* files error_email_to = jira-galaxy@blah error_email_from = galaxy-admin@blah I am attaching a zipper of the code changes. Thanks, Ann ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] GCC2012 Update
Hello all, The original email included a link to register for GCC2011. While, gosh, that was a great meeting, it might have been more helpful to provide you with the link to this year's registration link instead: http://wiki.g2.bx.psu.edu/Events/GCC2012/Register With apologies for the duplicate emails, Dave C. On Mon, May 14, 2012 at 1:13 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, The 2012 Galaxy Community Conference (GCC2012), being held in Chicago, Illinois, July 25-27, is *now just 10 weeks away*. We have updates on: 1. Help set the topics covered on Training Day (by this Friday) 2. Early registration closes June 11 3. Confirmed Speaker List As always, please let me know if you have any questions, and I hope to see you in Chicago! Thanks, Dave Clements on behalf of the GCC2012 Organizing Committee *1. Training Day Topics: Vote by this Friday * A day of tutorials has been added to the agenda this year. The GCC2012 Training Day has 3 parallel tracks, each featuring four, 90 minute workshops and covering between and 7 and 12 different topics. *Please take a few minutes to vote on topics that you would like to see presented: * http://bit.ly/GCC2012TDSurvey The survey ends this Friday, May 18, so please provide your feedback now. *2. Early Registration: Ends June 11 * The GCC2012 early registration is now just 4 weeks away. Registering early saves* 36 to 42%* on registration costs, and allows you to book discounted conference lodging before it fills up. *Register now at* http://galaxy.psu.edu/gcc2011/Register.html *3. Confirmed Speakers and Abstracts Posted * A list of confirmed speakers and abstracts are now available on the conference web site at http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers This list is not yet finished, but will give you a pretty accurate idea of the range of topics that will be discussed during the main meeting. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] May 2012 Galaxy Update
Hello all, The May 2012 Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05is now available ( http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05). *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates * is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates* complement the *Galaxy Development News Briefshttp://wiki.g2.bx.psu.edu/DevNewsBriefs * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - GCC2012: Just 3 Months Away!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#GCC2012:_Just_3_Months_Away.21 - Training Day needs your input!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#Training_Day:_We_Need_Your_Help.21 Please tell us what you want to be coveredhttps://docs.google.com/spreadsheet/viewform?formkey=dHBIRVB6cEhpTWpGN1pXSjhGdGR0aVE6MQ#gid=0. - Galaxy Tour de France 2012: This Month!http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#Galaxy_Tour_de_France_2012 - A new public server: Nebula for ChIP-Seqhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#New_Public_Server:_Nebula - 31 New Papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#Who.27s_Hiringat six different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#Upcoming_Events_and_Deadlines - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_05#Tool_Shed_Contributions As always, if you have anything you would like to see in the June *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates*, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Interested in speaking with other institutions deploying Galaxy locally?
Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I too like that it is user driven. And, while I am not a developer, I do plan on being on the call as often as possible. I can also offer my support for logistical and any other support. Ann, please let me know if you want help with getting this going and getting the word out. On a related note, With Matloob's email, we have at least 3 organizations in Australia and New Zealand that are interested. I know that there are many more Galaxy installations in that part of the world (and you have Enis and Ross in Australia now). Would this be a good opportunity to set up the first (to my knowledge) regional user group? If anyone thinks this is a good idea, please respond (and create a new thread). Finally, Ann, thanks for starting this. Dave C I also that both Ross and Enis are in Australia now On Sun, Apr 29, 2012 at 10:24 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Ryan, I like that it's user-directed, and we could be there to provide input, although if help is needed to organize the call we could probably assist with that. I plan to be on the call as often as my schedule allows, and I believe some of the other developers on the team would also be interested. --nate On Apr 28, 2012, at 8:49 AM, Ryan Golhar wrote: One question - Are the Galaxy developers involved in this or is this for user's only? It may be helpful to have developers on the call to provide information that users do not necessarily have. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] GCC2012 Abstract Submission Deadline is April 16, one week from today.
Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is TODAY. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, Dave C On Mon, Apr 9, 2012 at 2:03 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is April 16, one week from today. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, and hope to see you in Chicago, Dave C On Mon, Feb 13, 2012 at 3:27 PM, Dave Clements cleme...@galaxyproject.org wrote: Hello all, Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) http://wiki.g2.bx.psu.edu/Events/GCC2012. Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to: - Best practices for local Galaxy installation and management - Integrating tools and/or data sources into the Galaxy framework - Deploying galaxy on different infrastructures - Compelling or novel uses of Galaxy for biomedical analysis See the GCC2011 program http://wiki.g2.bx.psu.edu/Events/GCC2011 for an idea of the breadth of topics that can be covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts page for more details and how to submit. GCC2012 http://wiki.g2.bx.psu.edu/Events/GCC2012 will be held, July 25-27 in Chicago, Illinois, United States. The main meeting will run for two full days http://wiki.g2.bx.psu.edu/Events/GCC2012/Program, and be preceded by a full day of training workshopshttp://wiki.g2.bx.psu.edu/Events/GCC2012/Program. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is relevant to you. Registration will open in March. GCC2012 is hosted by the University of Illinois at Chicagohttp://uic.edu/, the University of Illinois at Urbana-Champaign http://illinois.edu/, and the Computation Institute http://www.ci.anl.gov/. Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/Events/GCC2012/Abstracts Thanks, Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] April 2012 Galaxy Update
Hello all, The April 2012 Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04is now available. *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complements the *Galaxy Development News Briefshttp://wiki.g2.bx.psu.edu/DevNewsBriefs * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papershttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#New_Papers - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Who.27s_Hiringat six different institutions - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Upcoming_Events_and_Deadlines - GCC2012 Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#GCC2012_Update, including - Abstract submission deadline is April 16. - Early registration is now open. - Tool Shed Contributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Tool_Shed_Contributions(at least 15 new repositories) If you have anything you would like to see in the May *Galaxy Updatehttp://wiki.g2.bx.psu.edu/GalaxyUpdates *, please let me know. Thanks, Dave C. -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] GCC2012 Early Registration is Now Open
Hello all, We are pleased to announce that early registrationhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Registerfor the 2012 Galaxy Community Conference (GCC2012)http://wiki.g2.bx.psu.edu/Events/GCC2012is now open. GCC2012 will be held July 25-27, at the UIC Forum http://www.uic.edu/depts/uicforum/, in Chicago, Illinois. The conference will feature two full dayshttp://wiki.g2.bx.psu.edu/Events/GCC2012/Programof presentations, discussions, lightning talks, and breakouts. We have also added a new full day of traininghttp://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDaythis year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: - Sequencing core facility staff - Bioinformatics core staff - Bioinformatics tool and workflow developers - Bioinformatics focused principal investigators and researchers - Data producers - Power bioinformatics users This event will help you with integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Registration http://wiki.g2.bx.psu.edu/Events/GCC2012/Register is very affordable this year, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodginghttp://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodgingcan also be booked. Low-cost rooms have been reserved on the UIC campushttp://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#James_Stuckel_Towers. You can also stay at the official conference hotelhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Crowne_Plaza_Chicago_Metro_Downtown, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register earlyhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Register, if you would like to stay in either. Finally, abstract submissionhttp://wiki.g2.bx.psu.edu/Events/GCC2012/Abstractsis also open, from now through April 16. Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts page for details. Looking forward to seeing you in Chicago! Dave Clements http://wiki.g2.bx.psu.edu/DaveClements, on behalf of the GCC2012 Organizing Committeehttp://wiki.g2.bx.psu.edu/Events/GCC2012/Organizing%20Committee PS: Please help get the word out! A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Reducing costs in Cloud Galaxy
Hi Enis, Greg, I've taken stuff from my this email, and previous conversations with Enis and put it in the wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning Please feel free to update/correct/enhance. Dave C. On Mon, Mar 19, 2012 at 2:58 PM, Enis Afgan eaf...@emory.edu wrote: Greg, Regarding the performance of different types of instances, I came across this and thought you might potentially find it useful: http://cloudharmony.com/benchmarks Enis On Mon, Mar 19, 2012 at 7:49 PM, Greg Edwards gedwar...@gmail.com wrote: Enis, Thanks. Will try that re the storage. Greg E On Mon, Mar 19, 2012 at 4:49 PM, Enis Afgan eaf...@emory.edu wrote: Hi Greg, On Mon, Mar 19, 2012 at 11:01 AM, Greg Edwards gedwar...@gmail.comwrote: Hi, I've got an implementation of some proteomics tools going well in Galaxy on AWS EC2 under Cloudman. Thanks for the help along the way. I need to drive the costs down a bit. I'm using an m1.large AMI and it's costing about $180 - $200 / month. This is about 55% storage and 45% instance costs. That's peanuts in some senses but for now we need to get it down so that it comes out of petty cash for the department, while the case is proven for it's use. I have a few questions and would appreciate ny insights .. 1. AWS has just released an m1.medium and m1.small instance type, which are 1/2 and 1/4 the cost of m1.large. http://aws.amazon.com/ec2/instance-types/ http://aws.amazon.com/ec2/pricing/ I tried the m1.small and m1.medium with the latest Cloudman AMI * *galaxy-cloudman-2011-03-22 (ami-da58aab3) All seemed to install ok, but the Tools took up tp 30 minutes to start execution on m1.medium, and never started on m1.small. m1.medium only added about 15% to run times compared with m1.large, can't say for m1.small. t1.micro does run (and for free in my Free Tier first year) but blows execution times out by a factor of about 3 which is too much. Has anyone tried these new Instance Types ? (m1.small/medium) I have no real experience with these instance types yet either so maybe someone else can chime in on this? 2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ? You can do this manually: 1. Start a new Galaxy cluster (ie, one you can easily delete later) 2. ssh into the master instance and delete whatever genomes you don't need/want (these are all located under /mnt/galaxyIndices) 3. Create a new EBS volume of size that'll fit whatever's left on the original volume, attach it and mount it 4. Copy over the data from the original volume to the new one while keeping the directory structure the same (rsync is probably the best tool for this) 5. Unmount detach the new volume; create a snapshot from it 6. For the cluster you want to keep around (while it is terminated), edit persistent_data.yaml in it's bucket on S3 and replace the existing snap ID for the galaxyIndices with the snapshot ID you got in the previous step 7. Start that cluster and you should have a file system from the new snapshot mounted. 8. Terminate delete the cluster you created in step 1 If you don't want to have to do this the first time around on your custom cluster, you can first try it with another temporary cluster and make sure it all works as expected and then move on to the real cluster. Best, Enis Using m1.small/medium and getting rid of the 700GB would being my costs down to say $50 / month which is ok. Thanks ! Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Tutorials for SICER
H.K., Are your questions related to Galaxy, or SICER? Galaxy doc is available at http://wiki.g2.bx.psu.edu/Learn. SICER doc is at http://home.gwu.edu/~wpeng/Software.htm. I don't think there is any particular doc on running SICER under Galaxy. Dave C. On Tue, Feb 28, 2012 at 1:14 AM, Vidya .H.K hvi...@ibab.ac.in wrote: Hi, I am exploring SICER peak calling tool for ChIP seq data analysis. Can anyone suggest me tutorial site for galaxy SICER tool?? Regards H.K.VIDYA ___ 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] HMMER wrappers
Hi Peter, I think hmmerscan has been wrapped, but there is a missing e in the repository name. Look for hmmscan in the toolshed. The description for it is: hmmscan, for searching pfam with AA seqs. also included is hmm datatypes although hmmbuild, etc. isnt included yetX ill try to finish the rest of the hmmer suite soon Does that help? Dave C. On Tue, Feb 28, 2012 at 2:31 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. 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/ -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] anyone using SFTP?
Hi Mattias, Posting to Galaxy-Dev, so others can see the question and response. Is there anyone using SFTP in a local Galaxy installation? I read that FTP is insecure because it sends the data and user credentials in plaint text. The short answer is yes. See. http://galaxy-development-list-archive.2308389.n4.nabble.com/template/NamlServlet.jtp?macro=search_pagenode=4077377query=ftp+sftp Dave C. I found a HOWTO on installing SFTP in ProFTPD: http://www.directadmin.com/forum/showthread.php?t=30607page=1 But I want to know if anyone is using SFTP. Thanks! Mattias -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] 2012 Galaxy Community Conference (GCC2012): Now Accepting Abstracts
Hello all, Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) http://wiki.g2.bx.psu.edu/Events/GCC2012. Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to: - Best practices for local Galaxy installation and management - Integrating tools and/or data sources into the Galaxy framework - Deploying galaxy on different infrastructures - Compelling or novel uses of Galaxy for biomedical analysis See the GCC2011 program http://wiki.g2.bx.psu.edu/Events/GCC2011 for an idea of the breadth of topics that can be covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts page for more details and how to submit. GCC2012 http://wiki.g2.bx.psu.edu/Events/GCC2012 will be held, July 25-27 in Chicago, Illinois, United States. The main meeting will run for two full days http://wiki.g2.bx.psu.edu/Events/GCC2012/Program, and be preceded by a full day of training workshopshttp://wiki.g2.bx.psu.edu/Events/GCC2012/Program. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is relevant to you. Registration will open in March. GCC2012 is hosted by the University of Illinois at Chicago http://uic.edu/, the University of Illinois at Urbana-Champaign http://illinois.edu/, and the Computation Institute http://www.ci.anl.gov/. Links: http://galaxyproject.org/GCC2012 http://galaxyproject.org/wiki/Events/GCC2012/Abstracts Thanks, Dave Clements -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] Galaxy Wiki
Hi John, (and every potential wiki contributor, which on the dev list is all of you :-) ** I apologize for missing your question back in December (and for not noticing it since, either). Thanks to Jen for refreshing the thread. 1. Thanks to your email, I have added your username and *107 others *to the Vetted Editors List (http://wiki.g2.bx.psu.edu/VettedEditorGroup). 2. *You (and 107 new friends!) will no longer have to answer textchas/captchas to update the wiki.* 3. Now that we have 140 vetted users on the wiki, I hope to see a flood of helpful updates there. :-) 4. For anyone who does not have an account on the wiki, and wants to update content, please create an account, send the username to me, and I will add you to vetted list. Again, I apologize for the delay. And, I would like to thank you for making me look at this. I had no idea we had that many logins on the wiki. Please let me know if you have any questions, Dave C. *Grinding Details, for those who care: * The Captcha questions are indeed darn irritating. We investigated all options currently available in MoinMoin, and unfortunately, they are the best choice. They also work very well at keeping out spam. They also apparently work very well at keeping out contributions. Some numbers: 198 Registered users on the wiki 32 of them were on the Vetted Editors List at the beginning of today 108 of them were added to the Vetted Editors List today, as a result of John's question. 58 of them are either blocked, known spammers, or I could not verify who they were. In the past, I have only added usernames to the Vetted Editor List, once the user had successfully made an edit. I am wondering if many of those 108 newly vetted users tried to update a page and were defeated by the captchas? In the future, I'll check the new user list, and update the vetted list once a month. On Tue, Jan 31, 2012 at 2:56 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi John, I am going to put you in touch with our wiki guru, Dave. Hopefully you two will be able to work out some sort of solution. I believe there is a super secret list he can add you to that will made the question burden much lighter (i.e. none). But with all sincerity, we really do appreciate the help, and look forward to your contributions, Best, Jen Galaxy team On 12/20/11 11:04 AM, John Major wrote: Galaxy team- I've tried a few times to add some content to the FAQ, but the captcha questions keep failing, or i'm submitting the wrong answer. I'd suggest a slightly less burdensome barrier to contributing- i'm certain this is dialing down your user contributions significantly. John __**_ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/**Supporthttp://galaxyproject.org/wiki/Support -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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] February 2012 Galaxy Update
Hello all, The inaugural edition http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02 of *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates* is now available. *Galaxy Update http://wiki.g2.bx.psu.edu/GalaxyUpdates* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates* will complement the *Galaxy Development News Briefshttp://wiki.g2.bx.psu.edu/DevNewsBriefs * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - New Papers http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Papers - New Public Server: MGTAXAhttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Public_Server:_MGTAXA - Open Positionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Who.27s_Hiring - Upcoming Events and Deadlineshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#Upcoming_Events_and_Deadlines - GCC2012 Sponsorshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#GCC2012_Sponsors - New Distributionshttp://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_02#New_Distributions If you have anything you would like to see in the March *Galaxy Update*, please let me know. Dave Clements Link: http://galaxyproject.org/wiki/GalaxyUpdates/2012_02 -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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 @ PAG 2012
Hello all, Plant and Animal Genome XX (PAG2012) starts in San Diego on January 14. If you are attending PAG then you will have (at least) a half-dozen opportunities to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the Galaxy @ PAG2012 page (http://wiki.g2.bx.psu.edu/Events/PAG2012) and the conference website (http://www.intlpag.org/) for more information. Dannon Baker and Dave Clements from the Galaxy Team ( http://wiki.g2.bx.psu.edu/Galaxy%20Team) will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself. Hope to see you in San Diego, Dave Clements and Dannon Baker -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ 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/
