Re: [galaxy-dev] FTP password and web interface password
Hi Nate, after severall modification before the week end, it finally worked out. I guess there was something in the configuration that I changed but I cannot say which one because of the number of trials... Thanks for helping. Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 14/03/2014 16:43, Nate Coraor a écrit : Hi Yec'han, Sorry for the delayed response - I would guess that something is different about the configuration of the SFTP server. Could you check the server logs? --nate On Thu, Mar 6, 2014 at 8:13 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi Nate, I have reseted the password of a newly created user, so now, it does not begin with $PBKDF2$. With the reseted password, I can access the web interface but I can not connect by SFTP. Here is the log of filezilla: Statut :Connexion à galaxy-pgtp.pierroton.inra.fr... Suivi :Going to execute /usr/bin/fzsftp Réponse :fzSftp started Suivi :CSftpControlSocket::ConnectParseResponse(fzSftp started) Suivi :CSftpControlSocket::SendNextCommand() Suivi :CSftpControlSocket::ConnectSend() Commande :open new_u...@mydomain.com@galaxy-pgtp.pierroton.inra.fr 22 Suivi :Server version: SSH-2.0-mod_sftp/0.9.8 Suivi :Using SSH protocol version 2 Suivi :We claim version: SSH-2.0-PuTTY_Local:_Sep_14_2013_01:12:43 Suivi :Doing Diffie-Hellman group exchange Suivi :Doing Diffie-Hellman key exchange with hash SHA-256 Suivi :Host key fingerprint is: Suivi :ssh-rsa *** Suivi :Initialised AES-256 SDCTR client-server encryption Suivi :Initialised HMAC-SHA1 client-server MAC algorithm Suivi :Initialised AES-256 SDCTR server-client encryption Suivi :Initialised HMAC-SHA1 server-client MAC algorithm Suivi :Pageant is running. Requesting keys. Suivi :Pageant has 1 SSH-2 keys Commande :Pass: ** Suivi :Sent password Suivi :Access denied Erreur :Échec de l'authentification. Suivi :CControlSocket::DoClose(1030) Suivi :CSftpControlSocket::ResetOperation(1094) Suivi :CControlSocket::ResetOperation(1094) Erreur :Erreur critique Erreur :Impossible d'établir une connexion au serveur Suivi :CFileZillaEnginePrivate::ResetOperation(1094) If I use my own account which has been created a long time ago (understand here that some updates of galaxy have been done since this time...), the password is not PBKDF2$ encrypted and I can access both the web interface and the sftp. The filezilla log here is similar to the one shown above but of course, I get an Access granted instead of denied. I don't understand why old accounts can connect whereas new ones cannot although passwords are not PBKDF2$. Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 05/03/2014 20:44, Nate Coraor a écrit : Hi Yec'han, Could you check that the 'password' column for the user in question in the 'galaxy_user' table in the database does not begin with $PBKDF2$? If not, do you have any debug logs from the FTP session and server that provide details on the failure? --nate On Wed, Mar 5, 2014 at 10:36 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hello, does anybody have any idea of what I can do to fix the problem? Maybe an update is required? I currently use the changeset: 11219:5c789ab4144a thanks Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 18/02/2014 08:39, Yec'han Laizet a écrit : Hi Bjoern, I indeed followed the wiki tutorial to set up my FTP service some time ago. It seems, as you suggest, that newly created users cannot connect by SFTP. I followed the fix by putting the use_pbkdf2 = False line just below the [app:main] and restarted the galaxy server. I have reseted a newly created user password but it still does not work. Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 17/02/2014 18:12, Björn Grüning a écrit : Hi Yec'han, please have a look at https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If you are running postgres and you only
[galaxy-dev] InterMine data import tools missing?
Hi, First let me apologize if this is not the right place to post this – I wasn't sure. It seems that the various InterMine tools under GetData (FlyMine, YeastMine, MouseMine, …) have gone missing from the main Galaxy site. Can they be restored? Thanks. Cheers, Joel -- Joel E. Richardson, Ph.D. Sr. Research Scientist Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, Maine 04609 207-288-6435 joel.richard...@jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Reorder Sam files
Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar* Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] I can't impersonate an user
Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reorder Sam files
Hi Alex, can you check if all dependencies are installed. Afaik Galaxy sets an env variable to point to the actual jar file. That env variable is missing and the constructed path to your picard executable is looking like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar. Hope that helps, Bjoern Am 17.03.2014 15:48, schrieb Alexander Kurze: Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar* Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] I can't impersonate an user
Hi Ricardo, My guess is that you're running into an issue that was fixed in 694411e94d9a. Can you verify the URL that's being pinged by the impersonate dropdown is (in)valid? If so, pulling from stable should fix your issues. -Dannon On Mon, Mar 17, 2014 at 11:24 AM, Perez, Ricardo ricky_...@neo.tamu.eduwrote: Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reorder Sam files
Hi Bjoern, thanks for your quick answer. My path to my picard is /home/galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/picard/bf1c3f9f8282/picardunfortunately I cannot find a env.sh in there. The env.sh is in the dependency folder /home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f The env.sh points to the right folder JAVA_JAR_PATH=/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f/jars; export JAVA_JAR_PATH Any suggestions? Alex On Mon, Mar 17, 2014 at 3:31 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Alex, can you check if all dependencies are installed. Afaik Galaxy sets an env variable to point to the actual jar file. That env variable is missing and the constructed path to your picard executable is looking like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar. Hope that helps, Bjoern Am 17.03.2014 15:48, schrieb Alexander Kurze: Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar* Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex ___ 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/ -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] inserting .js file for visualization with d3.js
Hi Lionel, One option is to place your js code into the visualization framework as shown here : https://wiki.galaxyproject.org/VisualizationsRegistry Once you have activated the framework, a button will be provided to run your js code on a certain dataset file format / tool output file format. Can you tell me what the output format of your tool is i.e. tabular file? Is you d3 code public? If so could you please share it? I hope this helps a bit. Feel free to ask further questions. Thanks Sam ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] http://toolshed.g2.bx.psu.edu/ is down?
Is http://toolshed.g2.bx.psu.edu/ down? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ is down?
Yes, both the test and main Galaxy Tool Sheds are temporarily unavailable due to a hardware move that is in progress. I just learned of this this morning, so I didn't get a chance to send out an announcement. Sorry for the inconvenience! We'll send another announcement as soon as the Tool Sheds are available. Greg Von Kuster On Mar 17, 2014, at 1:17 PM, changyu changyu_...@mail.dfci.harvard.edu wrote: Is http://toolshed.g2.bx.psu.edu/ down? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ is down?
Both the test and main Galaxy Tool Sheds should now be available. Please let us know if you encounter issues. Thanks, Greg Von Kuster On Mar 17, 2014, at 1:31 PM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, both the test and main Galaxy Tool Sheds are temporarily unavailable due to a hardware move that is in progress. I just learned of this this morning, so I didn't get a chance to send out an announcement. Sorry for the inconvenience! We'll send another announcement as soon as the Tool Sheds are available. Greg Von Kuster On Mar 17, 2014, at 1:17 PM, changyu changyu_...@mail.dfci.harvard.edu wrote: Is http://toolshed.g2.bx.psu.edu/ down? ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] inserting .js file for visualization with d3.js
Hi Sam, thank you very much for your clear answer. My output fil is a csv file. The d3 code is a kind of prototype for now.. but I can share at a later time.. what is the best way for that? Lionel 2014-03-17 17:14 GMT+01:00 sam guerler aysam.guer...@gmail.com: Hi Lionel, One option is to place your js code into the visualization framework as shown here : https://wiki.galaxyproject.org/VisualizationsRegistry Once you have activated the framework, a button will be provided to run your js code on a certain dataset file format / tool output file format. Can you tell me what the output format of your tool is i.e. tabular file? Is you d3 code public? If so could you please share it? I hope this helps a bit. Feel free to ask further questions. Thanks Sam ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] ToolSheds
Hi everyone, I am just wondering if there is some problems with: http://testtoolshed.g2.bx.psu.edu/ ? Getting operation time out from my galaxy stand-alone admin view when i try to search and browse tools, no response to ping neither. Thanks! CA ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] ToolSheds
Hi, Tool Shed was down today morning due to hardware relocation. It is up since cca 3pm (EST) today. For up to date info about Galaxy including the downtimes (both planned unplanned) please follow us on twitter. https://twitter.com/galaxyproject thanks for using Galaxy! Martin On Mon, Mar 17, 2014 at 12:46 PM, César Acevedo cesar.acev...@aomail.uab.cat wrote: Hi everyone, I am just wondering if there is some problems with: http://testtoolshed.g2.bx.psu.edu/ ? Getting operation time out from my galaxy stand-alone admin view when i try to search and browse tools, no response to ping neither. Thanks! CA ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
