From koenvanderdrift at gmail.com Sat Apr 16 11:46:38 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 16 Apr 2011 11:46:38 -0400 Subject: [Biococoa-dev] commit authorization Message-ID: Hope this list is still active :) I lost my authorization to commit some changes I made in a file. I recently changed Mac's so I guess my keys didn't copy over, and that old Mac is gone. Anyone can help with pointing out how to regenerate these keys? Thanks, - Koen. From schristley at mac.com Sat Apr 16 12:25:52 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 11:25:52 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: Message-ID: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> Hi Koen, Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org cheers Scott On Apr 16, 2011, at 10:46 AM, Koen van der Drift wrote: > Hope this list is still active :) > > I lost my authorization to commit some changes I made in a file. I recently changed Mac's so I guess my keys didn't copy over, and that old Mac is gone. > > Anyone can help with pointing out how to regenerate these keys? > > Thanks, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From schristley at mac.com Sat Apr 16 12:30:01 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 11:30:01 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: Message-ID: Oh, I should mention that the SVN repository has been restructured, with directories moved around. So if you have an old checkout with some modified files, you might want to checkout BioCocoa from scratch, then copy over your modified files. Scott On Apr 16, 2011, at 10:46 AM, Koen van der Drift wrote: > Hope this list is still active :) > > I lost my authorization to commit some changes I made in a file. I recently changed Mac's so I guess my keys didn't copy over, and that old Mac is gone. > > Anyone can help with pointing out how to regenerate these keys? > > Thanks, > > - Koen. > _______________________________________________ > Biococoa-dev mailing list > Biococoa-dev at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/biococoa-dev From koenvanderdrift at gmail.com Sat Apr 16 12:50:54 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 16 Apr 2011 12:50:54 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> Message-ID: On Apr 16, 2011, at 12:25 PM, Scott Christley wrote: > Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org Hi Scott, Thanks for your reply. I cannot locate on bioinformatics.org where to store the key. If I try to ftp (using Transmit) I am denied access, and on the website I cannot find it either. Thanks, - Koen. From schristley at mac.com Sat Apr 16 13:48:13 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 12:48:13 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> Message-ID: <633D6D3E-3254-40AB-8386-727DA06C693E@mac.com> You need to use ssh and/or sftp from the terminal. ssh username at bioinformatics.org and use your password to access. That will connect you to the machine, then go into the .ssh directory (it is hidden, use "ls -a" to see it), edit the authorized_keys file and cut/paste in your public key. If you did it right then, logout and do another ssh and it should not ask for password. Scott On Apr 16, 2011, at 11:50 AM, Koen van der Drift wrote: > > On Apr 16, 2011, at 12:25 PM, Scott Christley wrote: > >> Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org > > Hi Scott, > > Thanks for your reply. I cannot locate on bioinformatics.org where to store the key. If I try to ftp (using Transmit) I am denied access, and on the website I cannot find it either. > > Thanks, > > - Koen. From schristley at mac.com Sat Apr 16 13:53:02 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 12:53:02 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> Message-ID: On Apr 16, 2011, at 11:50 AM, Koen van der Drift wrote: > > On Apr 16, 2011, at 12:25 PM, Scott Christley wrote: > >> Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org > > Hi Scott, > > Thanks for your reply. I cannot locate on bioinformatics.org where to store the key. If I try to ftp (using Transmit) I am denied access, and on the website I cannot find it either. There is some info hidden away, but it mainly points to other sources of help. http://www.bioinformatics.org/wiki/Subversion Scott From koenvanderdrift at gmail.com Sat Apr 16 15:32:04 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 16 Apr 2011 15:32:04 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> Message-ID: <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> No luck so far: koen at CloverBook:~$ ssh-keygen Generating public/private rsa key pair. Enter file in which to save the key (/Users/koen/.ssh/id_rsa): Enter passphrase (empty for no passphrase): Enter same passphrase again: Your identification has been saved in /Users/koen/.ssh/id_rsa. Your public key has been saved in /Users/koen/.ssh/id_rsa.pub. koen at CloverBook:~$ ssh koen at bioinformatics.org ssh_exchange_identification: Connection closed by remote host In vvverbose mode: koen at CloverBook:~$ ssh -vvv koen at bioinformatics.org OpenSSH_5.2p1, OpenSSL 0.9.8l 5 Nov 2009 debug1: Reading configuration data /etc/ssh_config debug2: ssh_connect: needpriv 0 debug1: Connecting to bioinformatics.org [75.126.74.92] port 22. debug1: Connection established. debug1: identity file /Users/koen/.ssh/identity type -1 debug3: Not a RSA1 key file /Users/koen/.ssh/id_rsa. debug2: key_type_from_name: unknown key type '-----BEGIN' debug3: key_read: missing keytype debug2: key_type_from_name: unknown key type 'Proc-Type:' debug3: key_read: missing keytype debug2: key_type_from_name: unknown key type 'DEK-Info:' debug3: key_read: missing keytype debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug3: key_read: missing whitespace debug2: key_type_from_name: unknown key type '-----END' debug3: key_read: missing keytype debug1: identity file /Users/koen/.ssh/id_rsa type 1 debug1: identity file /Users/koen/.ssh/id_dsa type -1 ssh_exchange_identification: Connection closed by remote host I'll keep googling for a possible solution. - Koen. On Apr 16, 2011, at 1:53 PM, Scott Christley wrote: > > On Apr 16, 2011, at 11:50 AM, Koen van der Drift wrote: > >> >> On Apr 16, 2011, at 12:25 PM, Scott Christley wrote: >> >>> Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org >> >> Hi Scott, >> >> Thanks for your reply. I cannot locate on bioinformatics.org where to store the key. If I try to ftp (using Transmit) I am denied access, and on the website I cannot find it either. > > There is some info hidden away, but it mainly points to other sources of help. > > http://www.bioinformatics.org/wiki/Subversion > > Scott From schristley at mac.com Sat Apr 16 17:45:36 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 16:45:36 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> Message-ID: <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> Hmm, that's strange. If you don't have the keys setup then it should just ask for your password for bioinformatics.org, but it seems to be just disconnecting you. Are you able to login to your account on bioinformatics.org? http://www.bioinformatics.org/project/?group_id=318 When you first tried connecting with ssh, did it ask you about authenticity, some message like this: The authenticity of host 'bioinformatics.org (75.126.74.92)' can't be established. RSA key fingerprint is 18:b2:62:ee:00:76:74:94:c9:e5:e4:28:27:b5:92:14. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'bioinformatics.org,75.126.74.92' (RSA) to the list of known hosts. Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. Scott On Apr 16, 2011, at 2:32 PM, Koen van der Drift wrote: > No luck so far: > > koen at CloverBook:~$ ssh-keygen > Generating public/private rsa key pair. > Enter file in which to save the key (/Users/koen/.ssh/id_rsa): > Enter passphrase (empty for no passphrase): > Enter same passphrase again: > Your identification has been saved in /Users/koen/.ssh/id_rsa. > Your public key has been saved in /Users/koen/.ssh/id_rsa.pub. > > koen at CloverBook:~$ ssh koen at bioinformatics.org > ssh_exchange_identification: Connection closed by remote host > > In vvverbose mode: > > koen at CloverBook:~$ ssh -vvv koen at bioinformatics.org > OpenSSH_5.2p1, OpenSSL 0.9.8l 5 Nov 2009 > debug1: Reading configuration data /etc/ssh_config > debug2: ssh_connect: needpriv 0 > debug1: Connecting to bioinformatics.org [75.126.74.92] port 22. > debug1: Connection established. > debug1: identity file /Users/koen/.ssh/identity type -1 > debug3: Not a RSA1 key file /Users/koen/.ssh/id_rsa. > debug2: key_type_from_name: unknown key type '-----BEGIN' > debug3: key_read: missing keytype > debug2: key_type_from_name: unknown key type 'Proc-Type:' > debug3: key_read: missing keytype > debug2: key_type_from_name: unknown key type 'DEK-Info:' > debug3: key_read: missing keytype > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug3: key_read: missing whitespace > debug2: key_type_from_name: unknown key type '-----END' > debug3: key_read: missing keytype > debug1: identity file /Users/koen/.ssh/id_rsa type 1 > debug1: identity file /Users/koen/.ssh/id_dsa type -1 > ssh_exchange_identification: Connection closed by remote host > > I'll keep googling for a possible solution. > > - Koen. > > > On Apr 16, 2011, at 1:53 PM, Scott Christley wrote: > >> >> On Apr 16, 2011, at 11:50 AM, Koen van der Drift wrote: >> >>> >>> On Apr 16, 2011, at 12:25 PM, Scott Christley wrote: >>> >>>> Open a terminal and run the ssh-keygen program. That will generate public and private key files in your ~/.ssh directory. Then you need to put the public key in the ~/.ssh/authorized_keys file on bioinformatics.org >>> >>> Hi Scott, >>> >>> Thanks for your reply. I cannot locate on bioinformatics.org where to store the key. If I try to ftp (using Transmit) I am denied access, and on the website I cannot find it either. >> >> There is some info hidden away, but it mainly points to other sources of help. >> >> http://www.bioinformatics.org/wiki/Subversion >> >> Scott > From koenvanderdrift at gmail.com Sat Apr 16 18:19:37 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 16 Apr 2011 18:19:37 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> Message-ID: <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> On Apr 16, 2011, at 5:45 PM, Scott Christley wrote: > Hmm, that's strange. If you don't have the keys setup then it should just ask for your password for bioinformatics.org, but it seems to be just disconnecting you. Are you able to login to your account on bioinformatics.org? > > http://www.bioinformatics.org/project/?group_id=318 Yes, I can login, I have no problem with that. I actually emailed them to see if they can help me. Maybe there's something wrong on the server side. > > When you first tried connecting with ssh, did it ask you about authenticity, some message like this: > > The authenticity of host 'bioinformatics.org (75.126.74.92)' can't be established. > RSA key fingerprint is 18:b2:62:ee:00:76:74:94:c9:e5:e4:28:27:b5:92:14. > Are you sure you want to continue connecting (yes/no)? yes > Warning: Permanently added 'bioinformatics.org,75.126.74.92' (RSA) to the list of known hosts. I don't recall seeing that message. > > Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. > I don't have such a file. Interestingly, it recognizes my name when I try to ftp: koen at CloverBook:~$ ftp bioinformatics.org Connected to bioinformatics.org. 220---------- Welcome to Pure-FTPd [privsep] [TLS] ---------- 220-You are user number 1 of 50 allowed. 220-Local time is now 18:17. Server port: 21. 220-Only anonymous FTP is allowed here 220-IPv6 connections are also welcome on this server. 220 You will be disconnected after 15 minutes of inactivity. Name (bioinformatics.org:koen): 230 Anonymous user logged in Remote system type is UNIX. Using binary mode to transfer files. ftp> Thanks for thinking along. - Koen. From schristley at mac.com Sat Apr 16 18:25:51 2011 From: schristley at mac.com (Scott Christley) Date: Sat, 16 Apr 2011 17:25:51 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> Message-ID: <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> On Apr 16, 2011, at 5:19 PM, Koen van der Drift wrote: >> >> Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. >> > > I don't have such a file. That's confusing, you don't have a .ssh directory in your home directory? Scott From koenvanderdrift at gmail.com Sat Apr 16 18:52:57 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Sat, 16 Apr 2011 18:52:57 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> Message-ID: <11901E16-ED06-4B2C-9489-93DB9483D2AB@gmail.com> On Apr 16, 2011, at 6:25 PM, Scott Christley wrote: > > On Apr 16, 2011, at 5:19 PM, Koen van der Drift wrote: > >>> >>> Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. >>> >> >> I don't have such a file. > > That's confusing, you don't have a .ssh directory in your home directory? > > Scott > Yes, I do have that folder (with the keys), but not the known_hosts file: koen at CloverBook:~/.ssh$ ls -la total 16 drwx------ 4 koen koen 136 Apr 16 14:13 . drwxr-xr-x 48 koen koen 1632 Apr 16 14:12 .. -rw------- 1 koen koen 1743 Apr 16 15:29 id_rsa -rw-r--r-- 1 koen koen 403 Apr 16 15:29 id_rsa.pub - Koen. From koenvanderdrift at gmail.com Mon Apr 18 23:22:07 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Mon, 18 Apr 2011 23:22:07 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> Message-ID: <3DA81D89-441D-4B45-9A7C-A039841EAB77@gmail.com> I got it to work with the help of Jeff from Bioinformatics.org My initial checkout was anonymous, hence I could not commit. - Koen. On Apr 16, 2011, at 6:25 PM, Scott Christley wrote: > > On Apr 16, 2011, at 5:19 PM, Koen van der Drift wrote: > >>> >>> Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. >>> >> >> I don't have such a file. > > That's confusing, you don't have a .ssh directory in your home directory? > > Scott > From schristley at mac.com Mon Apr 18 23:35:06 2011 From: schristley at mac.com (Scott Christley) Date: Mon, 18 Apr 2011 22:35:06 -0500 Subject: [Biococoa-dev] commit authorization In-Reply-To: <3DA81D89-441D-4B45-9A7C-A039841EAB77@gmail.com> References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> <3DA81D89-441D-4B45-9A7C-A039841EAB77@gmail.com> Message-ID: Ah ha! Glad you got it figured out, you had me stumped. Though I still don't see why you couldn't ssh into bioinformatics.org, did that get worked out too? Scott On Apr 18, 2011, at 10:22 PM, Koen van der Drift wrote: > I got it to work with the help of Jeff from Bioinformatics.org My initial checkout was anonymous, hence I could not commit. > > - Koen. > > > On Apr 16, 2011, at 6:25 PM, Scott Christley wrote: > >> >> On Apr 16, 2011, at 5:19 PM, Koen van der Drift wrote: >> >>>> >>>> Maybe somehow it is remembering your host (same IP address as old computer?) and that is causing a problem. You can try deleting or moving the .ssh/known_hosts file, then try connecting with ssh. >>>> >>> >>> I don't have such a file. >> >> That's confusing, you don't have a .ssh directory in your home directory? >> >> Scott >> > From schristley at mac.com Mon Apr 18 23:43:03 2011 From: schristley at mac.com (Scott Christley) Date: Mon, 18 Apr 2011 22:43:03 -0500 Subject: [Biococoa-dev] deChellyMobile Message-ID: For you iPad developers out there, there is a skeleton of an iPad app in the SVN repository under Applications. I'm still working through some design ideas with another developer, but the basic idea is to provide a mobile front-end to a bioinformatics server for managing data, doing analysis, and running simulations. cheers Scott From koenvanderdrift at gmail.com Mon Apr 18 23:44:56 2011 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Mon, 18 Apr 2011 23:44:56 -0400 Subject: [Biococoa-dev] commit authorization In-Reply-To: References: <0611EC0C-138E-4B3F-99D2-28288D3AF3DD@mac.com> <94DBFD3C-6645-4224-A1F9-FBD9609D35C3@gmail.com> <11FEFCA0-1C91-48E3-BD95-B35923CEFE75@mac.com> <816C1C85-11E5-4EE9-AF03-E59C20CBAB40@gmail.com> <6E829D13-88D0-4564-AC5F-EAA59440CDD9@mac.com> <3DA81D89-441D-4B45-9A7C-A039841EAB77@gmail.com> Message-ID: <73B27DD0-2093-4E22-A618-842FB287E5A0@gmail.com> On Apr 18, 2011, at 11:35 PM, Scott Christley wrote: > Though I still don't see why you couldn't ssh into bioinformatics.org, did that get worked out too? Yep, that works too, they had to reset my account since it was blacklisted due to too many attempts :). - Koen.