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From: Dave C. G. H. D. <he...@gm...> - 2010-02-08 15:25:17
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Hi Scott,
I'm not a CMap admin, but from scanning the CMap administration
PerlDoc, I found:
Evidence type specific options
A single correspondence can be supported by any number of evidence
types, so it is necessary that these be ranked from "1" to N (where
lower numbers have precedence over higher). When multiple records
support a correspondence, only the highest ranking evidence will be
used when determining how to draw the correspondence line. If you
intend to use cmap_admin.pl tool to create correspondences for you
based on simple name/feature type comparisons, you should create a
special evidence to use just for that purpose (e.g., with the name
"Automated name-based" or something similar to flag it as a
machine-created/non-curated correspondence). Evidence type color will
only be used when NOT aggregating.
+ Rank:
The rank of the evidence relative to the others
+ Line Type (line_type):
How lines representing this evidence type will be drawn.
Values:
direct: Line directly from feature to feature.
indirect: Line that starts perpendicular to the map for a short distance
before traveling to the other feature.
ribbon: A ribbon is drawn that spans the top and bottom of each feature.
I'm guessing you want ribbon?
Dave C.
On Thu, Feb 4, 2010 at 6:33 AM, Scott Harding <the...@gm...> wrote:
> HI Dave and others,
>
> Sorry for sending this query again to the whole group. I did not
> get much response last time. In CMAP, is it possible to create image that
> shows big blocks of synteny (as shown in the attached image). I am able to
> show synteny using lines without any problems. It would be great to show big
> blocks of synteny in a shaded way.
>
> Please let me know if you have question.
>
>
> Thanks
> Scott
>
>
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--
Please keep responses on the list!
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
|
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From: Dave C. G. H. D. <he...@gm...> - 2010-02-04 17:29:38
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Hello all, Need a logo that tells people what your web site, database or GMOD component is about? If your resource needs a logo then the GMOD Logo Program (http://gmod.org/wiki/GMOD_Logo_Program) can help. I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like have a custom designed logo for their web site, database or GMOD component. The program pairs GMOD community members with students in advanced design classes at colleges and universities. This spring we will be working with a class at Linn-Benton Community College. Participants will meet several times (remotely) over a 3 week period, with the end result being a new logo for your resource. Participation is limited to non-profits, and costs US$75. If you are interested, please see http://gmod.org/wiki/GMOD_Logo_Program for additional details and requirements, and an application form. The program is accepting applications until March 1. Thanks, Dave Clements GMOD Help Desk PS: This program was inspired by ZFIN's success with its logo (see http://zfin.org). ZFIN's excellent logo was created by working with a design class at the University of Oregon. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_Logo_Program http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-01-29 22:23:18
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Hello all, I am pleased to announce that we are now accepting applications for: 2010 GMOD Summer School - Americas 6-9 May 2010 NESCent, Durham, NC, USA http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas This will be a hands-on multi-day course aimed at teaching new GMOD users/administrators how to get GMOD Components up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular GMOD Components. The course will be held May 6-9, at NESCent in Durham, NC. These components will be covered: * Apollo - genome annotation editor * Chado - a modular and extensible database schema * Galaxy - workflow system * GBrowse - the Generic Genome Browser * GBrowse_syn - A generic synteny browser * JBrowse - genome browser * MAKER - genome annotation pipeline * Tripal - web front end for Chado The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest). In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be placed on the waiting list. See the course page for details and an application link: http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas Thanks, Dave Clements GMOD Help Desk PS: We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists and the GMOD News page/RSS feed for updates. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Scott C. <sc...@sc...> - 2010-01-26 18:16:44
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Hi Scott, This is a good example of why you should always keep responses on the list, because I don't know the answer. Hopefully Ken will chime in. Scott On Tue, Jan 26, 2010 at 1:07 PM, Scott Harding <the...@gm...> wrote: > Hi Scott, > > Thanks a lot. I have attached a file that I was able to generate using > cmap. I am not sure how to configure the conf file to enable block shading. > Can you guide me to the information where I can find information? > > Thanks > Scott > > > > > On Tue, Jan 26, 2010 at 12:51 PM, Scott Cain <sc...@sc...> wrote: >> >> Hi Scott, >> >> With CMap, you can certainly get close. For example, the attached >> image shows synteny between a rice chromosome and a sorghum >> chromosome. The image is pretty "noisy", but that is because all of >> the data about relationships between the two chromosomes are included. >> The person who supplied the data could have decided to limit the >> number of correspondences to very few and resulted in a cleaner >> picture. >> >> Scott >> >> >> On Tue, Jan 26, 2010 at 11:41 AM, Scott Harding <the...@gm...> >> wrote: >> > >> > >> > Hi >> > >> > I was wondering if it is possible to produce images (with huge >> > blocks of synteny) as shown in the attached image. >> > >> > Thanks >> > >> > Scott >> > >> > >> >> >> >> -- >> ------------------------------------------------------------------------ >> Scott Cain, Ph. D. scott at scottcain >> dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Scott C. <sc...@sc...> - 2010-01-26 17:51:18
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Hi Scott, With CMap, you can certainly get close. For example, the attached image shows synteny between a rice chromosome and a sorghum chromosome. The image is pretty "noisy", but that is because all of the data about relationships between the two chromosomes are included. The person who supplied the data could have decided to limit the number of correspondences to very few and resulted in a cleaner picture. Scott On Tue, Jan 26, 2010 at 11:41 AM, Scott Harding <the...@gm...> wrote: > > > Hi > > I was wondering if it is possible to produce images (with huge > blocks of synteny) as shown in the attached image. > > Thanks > > Scott > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. G. H. D. <he...@gm...> - 2010-01-21 19:18:19
|
Hello all, Chris Duran gave an interesting talk on CMap3D (and other tools) at PAG 2010. CMap3D is a 3D comparative map viewer that runs on top of a standard CMap database backend. I've created a CMap3D page on the GMOD wiki with links to the CMap3D website, paper, and PAG presentation: http://gmod.org/wiki/CMap3D Dave C -- Please keep responses on the list! http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <he...@gm...> - 2010-01-06 19:23:23
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Hello all, GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego. There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. This includes workshops, talks, and posters on CMap: Development Of Tools For The Analysis And Visualisation Of Second Generation Sequencing Data For Brassica Species, Saturday, Jan 9, 11:40am-12:00pm, Golden West Room, Chris Duran Chris will be talking about CMap3D, a 3D version of CMap. P859: Visualizing And Comparing Genomes Monday, Jan 11, 3:00-4:30pm, Afternoon poster session, Ken Youens-Clark Find out about future development plans for CMap. Using Gramene: A Genomics and Genetics Resource for Rice and other Grasses Tuesday, Jan 12, California Room This will include a section on CMap, taught by Ken Youens-Clark (I think!) There will also be at least 7 other talks and posters by CMap users during PAG. See the PAG 2010 page on the GMOD wiki for a full listing and a flier showing highlights: http://gmod.org/wiki/PAG_2010 Thanks, Dave C. -- Please keep responses on the list! http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback |
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From: Ken Youens-C. <kyc...@gm...> - 2009-12-04 14:01:19
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On Dec 3, 2009, at 6:40 PM, ran...@bi... wrote: > We have been using an antiquated version of CMAP 0.12 on Oracle for a very long time, but now we are migrating to postgresql and would like to use the newer version of CMAP. I have the newest stable version, 1.0.1 installed, and I am uploading MAPS, but I can not find in the web based admin interface how to create new feature types like I could in the 0.12 version of CMAP. Can anyone point me in the right direction here. Is there a new and improved way of performing this task? I noticed that there is not even a feature_type table in the new version of CMAP? > > Thanks, > > Randall Svancara > Systems Administrator/DBA/Developer > Main Bioinformatics Laboratory Randall, Yes, you are correct. Around 0.14, I think, Ben Faga, the developer who took over CMap development for a few years, moved all the feature types into a config file. I believe map types also got moved. You should take a look at the sample configuration files. There are two you will need to edit, a "global.conf" for global settings and individual "datasource.conf" files for each datasource you want. Each datasource will have it's own feature/map types (just like they used to be inside the dbs). I believe the idea was to reduce the number of joins in SQL in order to improve performance. -- Ken Youens-Clark kc...@cs... Gramene.org Project Manager Ware Lab/CSHL/USDA-ARS |
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From: <ran...@bi...> - 2009-12-04 00:55:18
|
We have been using an antiquated version of CMAP 0.12 on Oracle for a very long time, but now we are migrating to postgresql and would like to use the newer version of CMAP. I have the newest stable version, 1.0.1 installed, and I am uploading MAPS, but I can not find in the web based admin interface how to create new feature types like I could in the 0.12 version of CMAP. Can anyone point me in the right direction here. Is there a new and improved way of performing this task? I noticed that there is not even a feature_type table in the new version of CMAP? Thanks, Randall Svancara Systems Administrator/DBA/Developer Main Bioinformatics Laboratory |
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From: Dave C. G. H. D. <he...@gm...> - 2009-11-14 20:26:11
|
Hello all,
A paper on CMap is in the current issue of Bioinformatics:
CMap 1.01: a comparative mapping application for the Internet,
by Ken Youens-Clark, Ben Faga, Immanuel V. Yap, Lincoln Stein
and Doreen Ware.
http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040
If you use CMap in your research, please reference it in your publications.
CMap will also be covered in the Gramene workshop
(http://www.intl-pag.org/18/18-gramene.html) at Plant and Animal
Genome (and in a poster as well). Watch http://gmod.org/wiki/PAG_2010
for a full list of GMOD related content at that meeting.
Dave Clements
GMOD Help Desk
--
Please keep responses on the list!
http://gmod.org/wiki/January_2010_GMOD_Meeting
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
|
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From: Scott C. <sc...@sc...> - 2009-11-13 14:48:51
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Hello, I am pleased to announce that the January GMOD meeting will be taking place on January 14 and 15 in San Diego at the Best Western Seven Seas (the same location as last year). Please see this page for registration information: http://gmod.org/wiki/January_2010_GMOD_Meeting When you go to that page, please take a moment to add suggestions for the agenda. There is no registration fee for this meeting, however there is limited space, so please register early. The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the GMOD meeting and the Plant and Animal Genome meeting before it may stay at the Best Western the entire time. Please direct follow up questions to the gmod-devel mailing list: https://lists.sourceforge.net/lists/listinfo/gmod-devel Thanks and I look forward to seeing you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Dave C. G. H. D. <gmo...@go...> - 2009-09-23 18:50:00
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Hello all, This is a final reminder that the 2009 GMOD Survey (and your chance to win GMOD gear) closes in two days, at the end of Friday, September 25. If you haven't already done so, please take a few minutes to fill out the survey at: http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009 And, if you have an interest in automatic text mining & publication curation tools such as Textpresso, the Biocurator community is running a survey on that topic at http://www.surveymonkey.com/s.aspx?sm=3tfC_2fq3h2bxoncUJES_2fjtg_3d_3d This survey was spawned by the "Text Mining for the BioCuration Workflow" workshop at the 2009 Biocuration Conference. See http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop1.html. (And, no, there is no free stuff, but it is a good cause.) Thanks, Dave C. On Wed, Sep 16, 2009 at 5:06 PM, Dave Clements, GMOD Help Desk <gmo...@go...> wrote: > Hello all, > > Please take a few minutes to fill out the 2009 GMOD Community Survey > and your name will be entered to win a free GMOD T-shirt or mug! This > year's survey focuses on genome and comparative genomics visualization > (and is much shorter than the 2008 survey). We are asking all GMOD > users and developers to provide feedback. > > http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009 > > Three randomly selected survey participants will receive the GMOD > T-shirt or mug of their choice. Names will be drawn from the first 100 > responses, so get your response in early. The survey closes at the end > of the day on September 25. > > Please contact the GMOD Help Desk if you have any questions. > > Thanks, > > Dave C > GMOD Help Desk > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > * GMOD News: http://gmod.org/wiki/GMOD_News > -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback * GMOD News: http://gmod.org/wiki/GMOD_News |
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From: Dave C. G. H. D. <gmo...@go...> - 2009-09-17 00:06:20
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Hello all, Please take a few minutes to fill out the 2009 GMOD Community Survey and your name will be entered to win a free GMOD T-shirt or mug! This year's survey focuses on genome and comparative genomics visualization (and is much shorter than the 2008 survey). We are asking all GMOD users and developers to provide feedback. http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009 Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice. Names will be drawn from the first 100 responses, so get your response in early. The survey closes at the end of the day on September 25. Please contact the GMOD Help Desk if you have any questions. Thanks, Dave C GMOD Help Desk -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback * GMOD News: http://gmod.org/wiki/GMOD_News |
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From: Dave C. G. H. D. <gmo...@go...> - 2009-09-15 23:51:30
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Hello all, GMOD's CVS projects were migrated to Subversion (SVN) today. For details, see * http://gmod.org/wiki/SVN * http://gmod.org/wiki/CVS_to_Subversion_Conversion Some important details: * Access to CVS is now read-only. * Inactive projects have been placed in the inactive subdirectory. * The website has been updated to reflect the move to SVN. * We've already identified a few outstanding issues. ** See http://gmod.org/wiki/CVS_to_Subversion_Conversion#Outstanding_Issues. ** If you find any more, please add them to the list or send the help desk an email. Please let us know if you have any questions. Thanks, Dave C and Rob B. -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback |
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From: Dave C. G. H. D. <gmo...@go...> - 2009-09-11 16:37:27
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Hello all, This is just a reminder that on Tuesday, September 15, Rob Buels will be moving GMOD's SourceForge source code repository from CVS to SVN. If you have checked out and modified any code from that repository, please commit your updates before 3am, Eastern US, on September 15. Some important bits: * All projects will be frozen in CVS and will remain available from CVS. * No new updates will be allowed in CVS. * All project will be moved to Subversion. * Inactive projects will be moved to a separate archival directory. See http://gmod.org/wiki/CVS_to_Subversion_Conversion for full details and a list of active and inactive projects. Thanks, Dave C -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback |
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From: Jacques-Gustave A. <au...@pi...> - 2009-09-09 07:18:43
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Thanks a lot!! Audrey Le mardi 08 septembre 2009 à 16:24 -0500, Ken Youens-Clark a écrit : > On Sep 8, 2009, at 3:59 AM, Jacques-Gustave Audrey wrote: > > > Dear all, > > > > The CMAP database have been moved to a new server in my laboratory. > > The > > application part of CMAP stay in the origin server. How is it possible > > to connect to the database on another server? > > > > I tried to change in the demo.conf file the lines corresponding to the > > database connection by adding: > > host new_server_name > > Audrey, > > Use this as a template for your datasource's configuration file: > > <database> > name MyDB > datasource dbi:mysql:host=new_server_name;database=cmap > user cmap > password ilikecake > is_default 1 > </database> > > -- > Ken Youens-Clark > kc...@cs... > Gramene.org Project Manager > Ware Lab/CSHL/USDA-ARS > > -- Jacques-Gustave Audrey <au...@pi...> |
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From: Ken Youens-C. <ky...@gm...> - 2009-09-08 21:24:25
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On Sep 8, 2009, at 3:59 AM, Jacques-Gustave Audrey wrote: > Dear all, > > The CMAP database have been moved to a new server in my laboratory. > The > application part of CMAP stay in the origin server. How is it possible > to connect to the database on another server? > > I tried to change in the demo.conf file the lines corresponding to the > database connection by adding: > host new_server_name Audrey, Use this as a template for your datasource's configuration file: <database> name MyDB datasource dbi:mysql:host=new_server_name;database=cmap user cmap password ilikecake is_default 1 </database> -- Ken Youens-Clark kc...@cs... Gramene.org Project Manager Ware Lab/CSHL/USDA-ARS |
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From: Jacques-Gustave A. <au...@pi...> - 2009-09-08 09:07:51
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Dear all, The CMAP database have been moved to a new server in my laboratory. The application part of CMAP stay in the origin server. How is it possible to connect to the database on another server? I tried to change in the demo.conf file the lines corresponding to the database connection by adding: host new_server_name But this doesn't work. Thank for your help. Best regards, Audrey -- Jacques-Gustave Audrey <au...@pi...> |
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From: Jacques-Gustave A. <au...@pi...> - 2009-09-08 09:07:37
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Dear all, The CMAP database have been moved to a new server in my laboratory. The application part of CMAP stay in the origin server. How is it possible to connect to the database on another server? I tried to change in the demo.conf file the lines corresponding to the database connection by adding: host new_server_name But this doesn't work. Thank for your help. Best regards, Audrey -- Jacques-Gustave Audrey <au...@pi...> |
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From: Robert B. <rm...@co...> - 2009-08-25 20:51:45
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OK, I moved the SVN copy of cmap from 'cmap' to 'cmap2'. I don't know how to do this in CVS, I suspect it's not really possible...anybody know? With no further action, on import day the CVS copy will end up as 'cmap' and the SVN copy will stay cmap2. We could move the cmap from CVS into cmap1 once it's in SVN though, that's easy. Rob Ken Youens-Clark wrote: > On Aug 25, 2009, at 3:09 PM, Robert Buels wrote: > >> A third option is to have the CVS cmap stuff go into 'cmap1' or >> something like that. Ken, if you want this option please tell me what >> directory name to use for the CVS copy. > > If you wanted to move everything in SVN to "cmap2" and move the CVS code > to "cmap1," that would be fine by me. I just made sure that everything > is commit to SVN if you wanted to move it around now. I won't be > hacking CMap for a bit until after Gramene is done with our next release. > > ky > -- Robert Buels Bioinformatics Analyst, Sol Genomics Network Boyce Thompson Institute for Plant Research Tower Rd Ithaca, NY 14853 Tel: 503-889-8539 rm...@co... http://www.sgn.cornell.edu |
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From: Ken Youens-C. <kyc...@gm...> - 2009-08-25 20:41:23
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On Aug 25, 2009, at 3:09 PM, Robert Buels wrote: > A third option is to have the CVS cmap stuff go into 'cmap1' or > something like that. Ken, if you want this option please tell me > what directory name to use for the CVS copy. If you wanted to move everything in SVN to "cmap2" and move the CVS code to "cmap1," that would be fine by me. I just made sure that everything is commit to SVN if you wanted to move it around now. I won't be hacking CMap for a bit until after Gramene is done with our next release. ky |
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From: Robert B. <rm...@co...> - 2009-08-25 20:10:20
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Scott Cain wrote: > For the time being, do you want to move your stuff currently in svn to a > directory like CMap2, or would you rather the current CMap cvs > repository not be migrated? A third option is to have the CVS cmap stuff go into 'cmap1' or something like that. Ken, if you want this option please tell me what directory name to use for the CVS copy. Rob |
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From: Scott C. <sc...@sc...> - 2009-08-25 16:13:22
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Hi Ken, For the time being, do you want to move your stuff currently in svn to a directory like CMap2, or would you rather the current CMap cvs repository not be migrated? Scott On Aug 25, 2009, at 10:07 AM, Ken Youens-Clark wrote: > On Aug 25, 2009, at 8:48 AM, Scott Cain wrote: > >> Hi Dave, Ken and Rob, >> >> This is the one that is going to give us trouble--Ken is using the >> gmod svn for developing the next version of CMap. Unless Ken says >> otherwise, we should leave the old CMap cvs repository where it is >> and leave the CMap svn repository the way it is too. >> >> Scott > > Scott, > > The CMap code in SVN is actually my version 2.0 experimental stuff. > I will need to move it to some other location so it won't get > clobbered by the old stuff getting moved in. > > ky ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Ken Youens-C. <kyc...@gm...> - 2009-08-25 14:07:18
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On Aug 25, 2009, at 8:48 AM, Scott Cain wrote: > Hi Dave, Ken and Rob, > > This is the one that is going to give us trouble--Ken is using the > gmod svn for developing the next version of CMap. Unless Ken says > otherwise, we should leave the old CMap cvs repository where it is > and leave the CMap svn repository the way it is too. > > Scott Scott, The CMap code in SVN is actually my version 2.0 experimental stuff. I will need to move it to some other location so it won't get clobbered by the old stuff getting moved in. ky |
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From: Scott C. <cai...@gm...> - 2009-08-25 13:56:13
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Hi Dave, Ken and Rob, This is the one that is going to give us trouble--Ken is using the gmod svn for developing the next version of CMap. Unless Ken says otherwise, we should leave the old CMap cvs repository where it is and leave the CMap svn repository the way it is too. Scott On Aug 24, 2009, at 7:50 PM, Dave Clements, GMOD Help Desk wrote: > Hello Ken, and the CMap community, > > On Sept 15, GMOD's CVS repository is moving to Subversion. Rob Buels > of Cornell is doing the heavy lifting. See below for details. > > Ken, I see that there are already both a CVS and SVN version of CMap. > Should Rob do anything to either version, or has CMap already > effectively been migrated to SVN? > > Thanks, > > Dave C. > > ---------- Forwarded message ---------- > From: Dave Clements, GMOD Help Desk <gmo...@go...> > Date: Mon, Aug 24, 2009 at 4:15 PM > Subject: CVS to SVN Conversion, 2009/09/15 > To: GMOD Announce <gmo...@li...>, GMOD > Developers <gmo...@li...> > Cc: Robert Buels <rm...@co...> > > > Hello all, > > Rob Buels of Cornell / SGN has offered to upgrade GMOD's source code > repositories to use Subversion (SVN) instead of CVS. After a two > month discussion on the GMOD Developers list (see > http://comments.gmane.org/gmane.science.biology.gmod.devel/364), this > update has been scheduled for September 15, 2009. > > If you are NOT a GMOD developer then this will, at most, change how > you get pre-release copies of GMOD components. In the future you will > do SVN checkouts instead of CVS checkouts. The doc on the web site > will be updated to describe how to do this. > > If you ARE a GMOD developer and your project is in GMOD's CVS > repository then please read the rest of this email carefully. > > > A complete list of projects in GMOD CVS is at > http://gmod.cvs.sourceforge.net/gmod/. Over the next two weeks we > will contact project developers to confirm what projects are still > active. All projects will be moved to SVN, but any projects that are > no longer active will then be deleted. A backup copy will exist in > SVN, but users, by default, will no longer see the deleted projects. > This should clean things up considerably. All projects will remain in > CVS as a read only archive. > > We have tentatively identified these projects as NO LONGER ACTIVE: > bop > citrina > gds > gmod > gmod-home > goet > graphbrowse > imdb > jalview > javaSean > labdoc > org.bdgp > pubfetch > pubtrack > sample_dbs > > There may be additional inactive projects as well. Again, we will > contact project developers before deleting any projects from SVN. > > Rob has created a preview version of the repository at > http://bugs.sgn.cornell.edu/trac/gmod_test_svn/browser/. Feel free to > poke around. This version does not have any projects removed from it. > > Rob will move the projects on September 15. Before then everyone with > uncommitted code changes should commit them to CVS. After September > 15, all CVS checkouts you have should be removed and new checkouts > made with SVN. We'll provide doc on how to do this. We will send out > exact details on the move a few days before it happens. > > > Please let Rob and I know if you have any questions. Again, we'll > send out a reminder and additional info a few days before the > conversion. > > Thanks, > > Dave Clements and Rob Buels > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > > > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > gmod-cmap mailing list > gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-cmap ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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