Re: [galaxy-user] [galaxy-dev] Connecting to new Galaxy Cloudman by FTP
FTP issues are fixed now so things will be functional out of the box without any of these workarounds. On Tue, Jul 16, 2013 at 4:04 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hey Mo, You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to create your instance, it should display an example connection string that will work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem ubuntu@IP', after your instance launched. Once inside of the machine, you can do something like: 'sudo -iu galaxy', to switch to the galaxy user and then have a look at the mount points under /mnt/. The cloudman_keypair.pem file is the key file that you (should have) downloaded the first time that you launched a cloudman instance, or when you manually generated a keypair. You can create additional keypairs in your aws console if you need to download a new one to use (you can probably delete the existing cloudman_keypair and have it regenerated automatically by cloudman, but I haven't tested this and I wouldn't recommend doing this if an instance is running). You'll need to use the correct .pem file for the keypair that you specified during launch of the instance. See http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/generating-a-keypair.htmlfor Amazon's info on creating keypairs (especially if you are using e.g. Windows and putty: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/putty.html). Once you make the changes to the files locally, you can use the Cloudman Admin web UI to restart the Galaxy instance. Let us know if you encounter any issues. Thanks for using Galaxy, Dan On Jul 15, 2013, at 7:22 PM, Mohammad Heydarian wrote: Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section, is telling me to change a setting of Cloudman by command line. This is generally where we get stuck in using Cloudman, because we aren't familiar with command line (we get cold sweats and light palpitations) and are weary of making changes to the Cloudman code. I would ask our IT guys for help, but their expertise ends at updating Office tools. I would bother a programmer or bioinformatician, but most of them are so busy you need a formal collaboration to get on their radar. I would ask people who vaguely know command line for help, but most of the time their knowledge of command line is just higher than mine and we end up troubleshooting an issue neither of us can really grasp. So, is there a webcast, or video, or slideshow, that can show a newbie how to command line into Cloudman and make the changes you outline in step 1? Cheers, Mo Heydarian On Mon, Jul 15, 2013 at 4:22 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Hey Mo, This may be a case of the new password hashing algorithm's incompatibility with the provided ProFTPD config. Could you try the following: 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section 2. Restart Galaxy 3. Reset your password in the Galaxy UI 4. Test FTP again --nate Cheers, Mo Heydarian ___ 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ The Galaxy User list should be
Re: [galaxy-user] [galaxy-dev] Connecting to new Galaxy Cloudman by FTP
Hey Mo, You can use ssh to connect to the Galaxy machine. If you used cloudlaunch to create your instance, it should display an example connection string that will work from e.g. a linux/mac shell, something like: 'ssh -i cloudman_keypair.pem ubuntu@IP', after your instance launched. Once inside of the machine, you can do something like: 'sudo -iu galaxy', to switch to the galaxy user and then have a look at the mount points under /mnt/. The cloudman_keypair.pem file is the key file that you (should have) downloaded the first time that you launched a cloudman instance, or when you manually generated a keypair. You can create additional keypairs in your aws console if you need to download a new one to use (you can probably delete the existing cloudman_keypair and have it regenerated automatically by cloudman, but I haven't tested this and I wouldn't recommend doing this if an instance is running). You'll need to use the correct .pem file for the keypair that you specified during launch of the instance. See http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/generating-a-keypair.html for Amazon's info on creating keypairs (especially if you are using e.g. Windows and putty: http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/putty.html). Once you make the changes to the files locally, you can use the Cloudman Admin web UI to restart the Galaxy instance. Let us know if you encounter any issues. Thanks for using Galaxy, Dan On Jul 15, 2013, at 7:22 PM, Mohammad Heydarian wrote: Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section, is telling me to change a setting of Cloudman by command line. This is generally where we get stuck in using Cloudman, because we aren't familiar with command line (we get cold sweats and light palpitations) and are weary of making changes to the Cloudman code. I would ask our IT guys for help, but their expertise ends at updating Office tools. I would bother a programmer or bioinformatician, but most of them are so busy you need a formal collaboration to get on their radar. I would ask people who vaguely know command line for help, but most of the time their knowledge of command line is just higher than mine and we end up troubleshooting an issue neither of us can really grasp. So, is there a webcast, or video, or slideshow, that can show a newbie how to command line into Cloudman and make the changes you outline in step 1? Cheers, Mo Heydarian On Mon, Jul 15, 2013 at 4:22 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Hey Mo, This may be a case of the new password hashing algorithm's incompatibility with the provided ProFTPD config. Could you try the following: 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section 2. Restart Galaxy 3. Reset your password in the Galaxy UI 4. Test FTP again --nate Cheers, Mo Heydarian ___ 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by
Re: [galaxy-user] [galaxy-dev] Connecting to new Galaxy Cloudman by FTP
Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section, is telling me to change a setting of Cloudman by command line. This is generally where we get stuck in using Cloudman, because we aren't familiar with command line (we get cold sweats and light palpitations) and are weary of making changes to the Cloudman code. I would ask our IT guys for help, but their expertise ends at updating Office tools. I would bother a programmer or bioinformatician, but most of them are so busy you need a formal collaboration to get on their radar. I would ask people who vaguely know command line for help, but most of the time their knowledge of command line is just higher than mine and we end up troubleshooting an issue neither of us can really grasp. So, is there a webcast, or video, or slideshow, that can show a newbie how to command line into Cloudman and make the changes you outline in step 1? Cheers, Mo Heydarian On Mon, Jul 15, 2013 at 4:22 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Hey Mo, This may be a case of the new password hashing algorithm's incompatibility with the provided ProFTPD config. Could you try the following: 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section 2. Restart Galaxy 3. Reset your password in the Galaxy UI 4. Test FTP again --nate Cheers, Mo Heydarian ___ 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
