From peter.schols at bio.kuleuven.ac.be Mon Jul 26 17:45:10 2004 From: peter.schols at bio.kuleuven.ac.be (Peter Schols) Date: Mon, 26 Jul 2004 23:45:10 +0200 Subject: [Biococoa-dev] test Message-ID: <1147F670-DF4D-11D8-A3E4-00039345483C@bio.kuleuven.ac.be> test From peter.schols at bio.kuleuven.ac.be Mon Jul 26 17:45:52 2004 From: peter.schols at bio.kuleuven.ac.be (Peter Schols) Date: Mon, 26 Jul 2004 23:45:52 +0200 Subject: [Biococoa-dev] test Message-ID: <2A2FAAF9-DF4D-11D8-A3E4-00039345483C@bio.kuleuven.ac.be> test From kvddrift at earthlink.net Mon Jul 26 19:03:19 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 26 Jul 2004 19:03:19 -0400 Subject: [Biococoa-dev] BioCocoa should be GUI-less (?) Message-ID: Hi, I was working on the addition of some code to BCCreator for other formats. Right now the panel with the popup showing the available formats is included in the framework. I don't think it is a good idea to put GUI elements in the framework, this should be the responsibility of the end user. An additional advantage is that the user can then dynamically decide which formats should be available in the popup maybe by using a plist file. What are others' opinions about this? I can work on changing this in the next couple of days if you guys agree. BTW, sorry for the cvs commits mess of Sunday. I'm pretty new to cvs and issued a cvs commit command, but didn't realize that all changed files in my sandbox would be commited instead of just the two I intended (StringAdditions.m and StringAdditions.h). I reverted some files, by actually updating them. If one of you knows how to revert all files I changed but those two, then please feel free to do so. - Koen. From mek at mekentosj.com Mon Jul 26 19:09:58 2004 From: mek at mekentosj.com (Alexander Griekspoor) Date: Tue, 27 Jul 2004 01:09:58 +0200 Subject: [Biococoa-dev] BioCocoa should be GUI-less (?) In-Reply-To: References: Message-ID: True, like my remark to stick to the appkit/foundation design, BioCocoa should be primarily a foundation framework. We could perhaps add an Appkit like part where one could optionally choose for a standard open/save panel (and sheet as option please ;-), like the addressbook peoplepicker. One thing I have made is a sheet/panel to allow direct searching and fetching of entrez nucleotide records, that could be another nice candidate for the BioCocoa appkit side... Alex Op 27-jul-04 om 1:03 heeft Koen van der Drift het volgende geschreven: > Hi, > > I was working on the addition of some code to BCCreator for other > formats. Right now the panel with the popup showing the available > formats is included in the framework. I don't think it is a good idea > to put GUI elements in the framework, this should be the > responsibility of the end user. An additional advantage is that the > user can then dynamically decide which formats should be available in > the popup maybe by using a plist file. > > What are others' opinions about this? I can work on changing this in > the next couple of days if you guys agree. > > > BTW, sorry for the cvs commits mess of Sunday. I'm pretty new to cvs > and issued a cvs commit command, but didn't realize that all changed > files in my sandbox would be commited instead of just the two I > intended (StringAdditions.m and StringAdditions.h). I reverted some > files, by actually updating them. If one of you knows how to revert > all files I changed but those two, then please feel free to do so. > > - Koen. > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* From james.balhoff at duke.edu Mon Jul 26 19:12:15 2004 From: james.balhoff at duke.edu (Jim Balhoff) Date: Mon, 26 Jul 2004 19:12:15 -0400 Subject: [Biococoa-dev] BioCocoa should be GUI-less (?) In-Reply-To: References: Message-ID: <3BEFAD4B-DF59-11D8-B572-000A95EECBDE@duke.edu> Hi, On Jul 26, 2004, at 7:03 PM, Koen van der Drift wrote: > Hi, > > I was working on the addition of some code to BCCreator for other > formats. Right now the panel with the popup showing the available > formats is included in the framework. I don't think it is a good idea > to put GUI elements in the framework, this should be the > responsibility of the end user. An additional advantage is that the > user can then dynamically decide which formats should be available in > the popup maybe by using a plist file. > > What are others' opinions about this? I can work on changing this in > the next couple of days if you guys agree. > I agree with this idea. I have thought about this also - it would be nice to be able to use the format conversion functionality without linking to AppKit. At least in past versions of Mac OS X, you could not run such a command line tool from a remote ssh session without being also logged in at the console. There could be a method which returned available formats, similar to +imageFileTypes provided by NSImage (the types returned by this method will include those added to the system by third party bundles; we could have sequence format plug-ins as well). - Jim ____________________________________________ James P. Balhoff Dept. of Biology Duke University Durham, NC 27708-0338 USA -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2373 bytes Desc: not available URL: From kvddrift at earthlink.net Mon Jul 26 19:25:16 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Mon, 26 Jul 2004 19:25:16 -0400 Subject: [Biococoa-dev] BioCocoa should be GUI-less (?) In-Reply-To: References: Message-ID: <0D55429A-DF5B-11D8-8235-003065A5FDCC@earthlink.net> On Jul 26, 2004, at 7:09 PM, Alexander Griekspoor wrote: > One thing I have made is a sheet/panel to allow direct searching and > fetching of entrez nucleotide records, that could be another nice > candidate for the BioCocoa appkit side... Yes, I like that too (and am already using something similar in my app). And again, easily extendible by making a popup with various servers (SwissProt, NCBI, maybe even local ones). The popup is build from a plist with all the server info. - Koen. From james.balhoff at duke.edu Tue Jul 27 23:02:29 2004 From: james.balhoff at duke.edu (Jim Balhoff) Date: Tue, 27 Jul 2004 23:02:29 -0400 Subject: [Biococoa-dev] Re: BioCocoa class structure In-Reply-To: References: Message-ID: <9023EF48-E042-11D8-8A62-000A95EECBDE@duke.edu> On Jul 27, 2004, at 10:27 PM, John Timmer wrote: > Okay, here's a possible class structure for your comment and > correction. > > For the immediate future, I'd imagine that the issue will more be > deciding > which class to put methods that we already have written into. > > And I checked out from CVS anonymously, so I'll try to comment some > code and > generate one of the Util classes.... > Just a small suggestion - I think we should try to make the class names (and organization) fit the Cocoa spirit as much as possible, so maybe the Display classes should be called more like "BCSequenceView", "BCChromatogramView", etc. Otherwise, I don't think of file IO immediately when I think of a sequence. Could there be a separate sequence class, which is used for analyses and could return various file type string representations when asked? I don't really have any experience designing an API, though, so feel free to disagree! ;-) - Jim ____________________________________________ James P. Balhoff Dept. of Biology Duke University Durham, NC 27708-0338 USA -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2373 bytes Desc: not available URL: From kvddrift at earthlink.net Wed Jul 28 06:11:30 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Wed, 28 Jul 2004 06:11:30 -0400 Subject: [Biococoa-dev] Re: BioCocoa class structure In-Reply-To: <9023EF48-E042-11D8-8A62-000A95EECBDE@duke.edu> References: <9023EF48-E042-11D8-8A62-000A95EECBDE@duke.edu> Message-ID: <7F04B0BA-E07E-11D8-8235-003065A5FDCC@earthlink.net> On Jul 27, 2004, at 11:02 PM, Jim Balhoff wrote: > Otherwise, I don't think of file IO immediately when I think of a > sequence. Could there be a separate sequence class, which is used for > analyses and could return various file type string representations > when asked? > I think that is a good suggestion. The current BCReader and BCCreator can be used as a starting point for that. I had a brief glance at the class structure and the file ideas document that John posted. First impression: very ambitious! I will read it more carefully, but have one first comment. Generally it is not recommended (if you check the cocoa mailinglists) to subclass foundation classes, such as NSDictionary. It is better to create a class that has an member of such a class. So in this case there would be a BCSequence class with a NS(Mutable)Dictionary as a member variable. - Koen. From jtimmer at bellatlantic.net Fri Jul 30 18:20:57 2004 From: jtimmer at bellatlantic.net (John Timmer) Date: Fri, 30 Jul 2004 18:20:57 -0400 Subject: [Biococoa-dev] CVS problems Message-ID: Sorry about this - I had problems logging into the CVS server, and wound up resetting my password (basic stupidity), which I've discovered changes my account in a way that eliminates the CVS privileges you gave me. I'm in the process of creating a few files and adding one of my own string additions to that file, so if you could re-grant me commit permissions, I'd appreciate it. Sorry about that, John _______________________________________________ This mind intentionally left blank From kvddrift at earthlink.net Fri Jul 30 18:47:23 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jul 2004 18:47:23 -0400 Subject: [Biococoa-dev] CVS problems In-Reply-To: References: Message-ID: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> On Jul 30, 2004, at 6:20 PM, John Timmer wrote: > 'm in the process of > creating a few files and adding one of my own string additions to that > file, > so if you could re-grant me commit permissions, I'd appreciate it. John, If you want, in the meantime I can commit the files for you. - Koen. From mek at mekentosj.com Fri Jul 30 19:00:15 2004 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 31 Jul 2004 01:00:15 +0200 Subject: [Biococoa-dev] CVS problems In-Reply-To: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> Message-ID: <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> I'm having some difficulties as well; does "cvs server: WARNING: global `-l' option ignored. ? BioCocoa.pbproj/griek.mode1 ? BioCocoa.pbproj/griek.pbxuser cvs [update aborted]: -t/-f wrappers not supported by this version of CVS " seem familiar to anyone of you guys? I try to update from within XCode. I vaguely remember that you somewhere had to set a list of extensions which CVS would see as wrappers, but perhaps you guys know as you seem to have it working... Cheers, Alex Op 31-jul-04 om 0:47 heeft Koen van der Drift het volgende geschreven: > > On Jul 30, 2004, at 6:20 PM, John Timmer wrote: > >> 'm in the process of >> creating a few files and adding one of my own string additions to >> that file, >> so if you could re-grant me commit permissions, I'd appreciate it. > > John, > > If you want, in the meantime I can commit the files for you. > > - Koen. > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > ************************************************************** ** Alexander Griekspoor ** ************************************************************** The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** From mek at mekentosj.com Fri Jul 30 19:08:34 2004 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 31 Jul 2004 01:08:34 +0200 Subject: [Biococoa-dev] CVS problems In-Reply-To: <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> Message-ID: <6165B8C8-E27D-11D8-A7E8-000393CFDE0C@mekentosj.com> Ok, seems to be a common thing: http://www.cocoadev.com/index.pl?CvsWrappers I'll have a look after I return from a weekend away and see if I can get my CVS to work again... Alex Op 31-jul-04 om 1:00 heeft Alexander Griekspoor het volgende geschreven: > I'm having some difficulties as well; does "cvs server: WARNING: > global `-l' option ignored. > ? BioCocoa.pbproj/griek.mode1 > ? BioCocoa.pbproj/griek.pbxuser > cvs [update aborted]: -t/-f wrappers not supported by this version of > CVS > " seem familiar to anyone of you guys? I try to update from within > XCode. I vaguely remember that you somewhere had to set a list of > extensions which CVS would see as wrappers, but perhaps you guys know > as you seem to have it working... > Cheers, > Alex > > Op 31-jul-04 om 0:47 heeft Koen van der Drift het volgende geschreven: > >> >> On Jul 30, 2004, at 6:20 PM, John Timmer wrote: >> >>> 'm in the process of >>> creating a few files and adding one of my own string additions to >>> that file, >>> so if you could re-grant me commit permissions, I'd appreciate it. >> >> John, >> >> If you want, in the meantime I can commit the files for you. >> >> - Koen. >> >> _______________________________________________ >> Biococoa-dev mailing list >> Biococoa-dev at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/biococoa-dev >> >> > ************************************************************** > ** Alexander Griekspoor ** > ************************************************************** > The Netherlands Cancer Institute > Department of Tumorbiology (H4) > Plesmanlaan 121, 1066 CX, Amsterdam > Tel: + 31 20 - 512 2023 > Fax: + 31 20 - 512 2029 > AIM: mekentosj at mac.com > E-mail: a.griekspoor at nki.nl > Web: http://www.mekentosj.com > > MacOS X: The power of UNIX with the simplicity of the Mac > > *************************************************************** > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > ************************************************************** ** Alexander Griekspoor ** ************************************************************** The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 AIM: mekentosj at mac.com E-mail: a.griekspoor at nki.nl Web: http://www.mekentosj.com MacOS X: The power of UNIX with the simplicity of the Mac *************************************************************** From kvddrift at earthlink.net Fri Jul 30 19:27:23 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jul 2004 19:27:23 -0400 Subject: [Biococoa-dev] CVS problems In-Reply-To: <6165B8C8-E27D-11D8-A7E8-000393CFDE0C@mekentosj.com> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> <6165B8C8-E27D-11D8-A7E8-000393CFDE0C@mekentosj.com> Message-ID: <02880544-E280-11D8-8553-003065A5FDCC@earthlink.net> On Jul 30, 2004, at 7:08 PM, Alexander Griekspoor wrote: > Ok, seems to be a common thing: > http://www.cocoadev.com/index.pl?CvsWrappers > I'll have a look after I return from a weekend away and see if I can > get my CVS to work again... > So far I have not been able to use CVS from Xcode. For now I just use the command line. This page has a good introduction: . - Koen. From mek at mekentosj.com Fri Jul 30 19:30:22 2004 From: mek at mekentosj.com (Alexander Griekspoor) Date: Sat, 31 Jul 2004 01:30:22 +0200 Subject: [Biococoa-dev] CVS problems In-Reply-To: <02880544-E280-11D8-8553-003065A5FDCC@earthlink.net> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> <6165B8C8-E27D-11D8-A7E8-000393CFDE0C@mekentosj.com> <02880544-E280-11D8-8553-003065A5FDCC@earthlink.net> Message-ID: <6D5D53D7-E280-11D8-A7E8-000393CFDE0C@mekentosj.com> I did have it working fine about a month ago, only now it's starts to complain. I really liked the easy access from within XCode.... I'll let you know if I find out more. Alex Op 31-jul-04 om 1:27 heeft Koen van der Drift het volgende geschreven: > > On Jul 30, 2004, at 7:08 PM, Alexander Griekspoor wrote: > >> Ok, seems to be a common thing: >> http://www.cocoadev.com/index.pl?CvsWrappers >> I'll have a look after I return from a weekend away and see if I can >> get my CVS to work again... >> > > So far I have not been able to use CVS from Xcode. For now I just use > the command line. This page has a good introduction: > . > > > - Koen. > > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/biococoa-dev > > ********************************************************* ** Alexander Griekspoor ** ********************************************************* The Netherlands Cancer Institute Department of Tumorbiology (H4) Plesmanlaan 121, 1066 CX, Amsterdam Tel: + 31 20 - 512 2023 Fax: + 31 20 - 512 2029 E-mail: a.griekspoor at nki.nl AIM: mekentosj at mac.com Web: http://www.mekentosj.com EnzymeX - To cut or not to cut http://www.mekentosj.com/enzymex ********************************************************* From kvddrift at earthlink.net Fri Jul 30 19:40:57 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jul 2004 19:40:57 -0400 Subject: [Biococoa-dev] CVS problems In-Reply-To: References: Message-ID: On Jul 30, 2004, at 6:54 PM, John Timmer wrote: > Thanks! I've attached the string additions, and a couple methods I > wrote to > help with a CGI program I was working on (modified for bioCocoa). If > you > could create a BCUtil group within the project, I've got another file > to add > to that later today (for now, my wife tells me it's time to go home for > dinner, so it'll be quite a bit later). > OK, done. I have put all four files into BCUtils. We probably should rename StringAdditions to BCStringUtils. - Koen. From jtimmer at bellatlantic.net Fri Jul 30 20:53:19 2004 From: jtimmer at bellatlantic.net (John Timmer) Date: Fri, 30 Jul 2004 20:53:19 -0400 Subject: [Biococoa-dev] CVS problems In-Reply-To: <38C7B9A0-E27C-11D8-8B66-003065D0AD9E@bio.kuleuven.ac.be> Message-ID: > Hi John and others, > > I have looked at the CVS permissions page and it appears that everyone > has CVS write permissions. What should I do now? > peter > Maybe I'm completely off, but I had assumed that the CVS password would be the same as my shell account, which should be the same as what logs me into the bioinformatics.org website. That, however, doesn't seem to be working. What have I done wrong? JT _______________________________________________ This mind intentionally left blank From kvddrift at earthlink.net Fri Jul 30 22:38:48 2004 From: kvddrift at earthlink.net (Koen van der Drift) Date: Fri, 30 Jul 2004 22:38:48 -0400 Subject: [Biococoa-dev] CVS problems In-Reply-To: References: Message-ID: On Jul 30, 2004, at 8:53 PM, John Timmer wrote: > Maybe I'm completely off, but I had assumed that the CVS password > would be > the same as my shell account, which should be the same as what logs me > into > the bioinformatics.org website. That, however, doesn't seem to be > working. > This is what Peter send me when I set up my account. Maybe that helps. I still need to try out the Xcode part at the end. - Koen. ================ - Launch the terminal and enter bash (or set the default shell to bash in the Terminal prefs) - Set two shell parameters by entering in the terminal: export CVS_RSH='ssh' export CVSROOT=':ext:loginname at bioinformatics.org:/cvsroot' (make sure to replace loginname by your login) - Create a folder on your machine where you want to store the BioCocoa source e.g. mkdir ~/Desktop/BioCocoa - Move to that folder e.g. cd ~/Desktop/BioCocoa - Move the contents of the CVS repository to that folder cvs checkout BioCocoa - The entire BioCocoa project will be transfered to your local folder. We are almost done but make sure to read the NeXT step. - There is one more thing you should do in order to make Xcode work with the CVS repository over ssh: If you?d like to use ssh without having to type your password every time (useful if you are accessing CVS via Xcode, for example), you?ll want to create a public/private key pair with the ssh-keygen command. The advantage of doing this is that your scripts will be able to run without human intervention. The disadvantage is that anyone who can access your account on your local Mac OS X box will also be able to access those remote servers which have stored your public key. In the terminal enter: ssh-keygen -t dsa -> Enter file in which to save the key (you can choose the proposed file name and path): -> Enter passphrase: hit return when you are asked for a passphrase -> Enter same passphrase again hit return a second time -> Your identification has been saved in /Users/peter/.ssh/id_dsa. -> Your public key has been saved in /Users/peter/.ssh/id_dsa.pub. Once you have created your private and public keys, you need to place your public key on the remote host in a place where ssh and scp can recognize it. Use ssh to connect to the remote host(s) on which you want to publish your projects. Then add the contents of your local ~/.ssh/identity.pub or id_dsa.pub file to a file in your remote ~/.ssh directory called ?authorized_keys? (if you don?t have one already, you can create it). You can od this by SFTPing to your bioinformattics account and by creating a .ssh folder in your Home directory and by adding a authorized_keys file to this dir. This way, you will be able to connect to the CVS server without entering a password. More importantly, Xcode will be able to connect to the CVS server without problems. Now you can open the project in Xcode and use the built-in SCM to work on the project. I'd recommend a CVS tutorial, e.g. http://www.linux.ie/articles/tutorials/cvs.php if you are not familiar with CVS. From peter.schols at bio.kuleuven.ac.be Sat Jul 31 04:39:16 2004 From: peter.schols at bio.kuleuven.ac.be (Peter Schols) Date: Sat, 31 Jul 2004 10:39:16 +0200 Subject: [Biococoa-dev] CVS problems In-Reply-To: <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> Message-ID: <1B789D0A-E2CD-11D8-A3E4-00039345483C@bio.kuleuven.ac.be> Hi All, Yesterday, I have sent a reply to John's post about CVS problems. Today I got a message stating that the post did not get through because the attach was too large. In summary, the messages and the attach showed that every BC developer registered at bioinformatics.org has CVS write permissions. So that can't be the source of the problems some of you are experiencing. In case some of you haven't received my CVS instructions yet, I have pasted them again at the end of this mail. I'm sorry for the delay in replying, I'm rebuilding our house right now, so I can't use my mac too often these days. :-( All the best, peter ----------------- - Launch the terminal and enter bash (or set the default shell to bash in the Terminal prefs) - Set two shell parameters by entering in the terminal: export CVS_RSH='ssh' export CVSROOT=':ext:loginname at bioinformatics.org:/cvsroot' (make sure to replace loginname by your login) - Create a folder on your machine where you want to store the BioCocoa source e.g. mkdir ~/Desktop/BioCocoa - Move to that folder e.g. cd ~/Desktop/BioCocoa - Move the contents of the CVS repository to that folder cvs checkout BioCocoa - The entire BioCocoa project will be transfered to your local folder. We are almost done but make sure to read the NeXT step. - There is one more thing you should do in order to make Xcode work with the CVS repository over ssh: If you?d like to use ssh without having to type your password every time (useful if you are accessing CVS via Xcode, for example), you?ll want to create a public/private key pair with the ssh-keygen command. The advantage of doing this is that your scripts will be able to run without human intervention. The disadvantage is that anyone who can access your account on your local Mac OS X box will also be able to access those remote servers which have stored your public key. In the terminal enter: ssh-keygen -t dsa -> Enter file in which to save the key (you can choose the proposed file name and path): -> Enter passphrase: hit return when you are asked for a passphrase -> Enter same passphrase again hit return a second time -> Your identification has been saved in /Users/peter/.ssh/id_dsa. -> Your public key has been saved in /Users/peter/.ssh/id_dsa.pub. Once you have created your private and public keys, you need to place your public key on the remote host in a place where ssh and scp can recognize it. Use ssh to connect to the remote host(s) on which you want to publish your projects. Then add the contents of your local ~/.ssh/identity.pub or id_dsa.pub file to a file in your remote ~/.ssh directory called ?authorized_keys? (if you don?t have one already, you can create it). You can od this by SFTPing to your bioinformattics account and by creating a .ssh folder in your Home directory and by adding a authorized_keys file to this dir. This way, you will be able to connect to the CVS server without entering a password. More importantly, Xcode will be able to connect to the CVS server without problems. Now you can open the project in Xcode and use the built-in SCM to work on the project. I'd recommend a CVS tutorial, e.g. http://www.linux.ie/articles/tutorials/cvs.php if you are not familiar with CVS. From james.balhoff at duke.edu Sat Jul 31 12:42:56 2004 From: james.balhoff at duke.edu (Jim Balhoff) Date: Sat, 31 Jul 2004 11:42:56 -0500 Subject: [Biococoa-dev] CVS problems In-Reply-To: <1B789D0A-E2CD-11D8-A3E4-00039345483C@bio.kuleuven.ac.be> References: <6BECB886-E27A-11D8-8553-003065A5FDCC@earthlink.net> <38494896-E27C-11D8-A7E8-000393CFDE0C@mekentosj.com> <1B789D0A-E2CD-11D8-A3E4-00039345483C@bio.kuleuven.ac.be> Message-ID: On Jul 31, 2004, at 3:39 AM, Peter Schols wrote: > > - There is one more thing you should do in order to make Xcode work > with the CVS repository over ssh: > If you?d like to use ssh without having to type your password every > time (useful if you are accessing CVS via Xcode, for example), you?ll > want to create a public/private key pair with the ssh-keygen command. > The advantage of doing this is that your scripts will be able to run > without human intervention. The disadvantage is that anyone who can > access your account on your local Mac OS X box will also be able to > access those remote servers which have stored your public key. There is another way to do this, which works very well. Use SSHPassKey to store your password in the Mac OS X keychain. It can be configured so that Xcode will use this to get the cvs password (you don't need to install the Project Builder plug-in mentioned in the ReadMe). Look here: - Jim ____________________________________________ James P. Balhoff Dept. of Biology Duke University Durham, NC 27708-0338 USA -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 2373 bytes Desc: not available URL: