[galaxy-dev] python: error while loading shared libraries

Dear Galaxy community, I'm currently testing cross-platform compatibility with our Galaxy instance (15.10) : - [on PROD environment] Galaxy service runs on a RedHat 6.5 server (using python2.6 installed in a virtualenv) and submits jobs on cluster nodes also in RedHat 6.5/python2.6 (default versi

[galaxy-dev] psycopg2 module and SSL connection to postgresql

Hi Galaxy Community, I have the same problem than Nikolay few years ago ( http://dev.list.galaxyproject.org/connecting-to-a-DB-on-a-different-host-td4139952.html#a4139955) : I would like to connect my Galaxy instance to my postgresql database using SSL encryption and Auth method md5. I have no pro

[galaxy-dev] Addind new datatype - best practice

Hi Galaxy community, I would like to add custom datatypes to my Galaxy server without editing any Galaxy files if possible. I've already created and renamed a second config/datatype.conf file. Both files are listed into galaxy.ini (variable datatypes_config_file). But what about the new datatype C

Re: [galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

sible. You can rename it once > On Fri, Oct 7, 2016 at 12:31 PM Floreline TOUCHARD < > floreline.touch...@gmail.com> wrote: > >> Hello Community, >> >> When I use the paste/fetch functionality to download data, the filename >> is display as "Pasted Entry&q

[galaxy-dev] Paste/Fetch data, indicate filename before download data (default = Pasted Entry)

Hello Community, When I use the paste/fetch functionality to download data, the filename is display as "Pasted Entry" into my history panel. Is it possible to indicate the filename I would like to be display into the history before the download ? I can see an edit button into the upload window bu

[galaxy-dev] IE11 display problem

Hi Galaxy team, I try to use IE11 but I have a problem with the display : I get a blank Web page (I can only see the logo and "Galaxy" on the tab) . The javascript console gives me the same errors as described here ( https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-July/020078.html). Mo

[galaxy-dev] Load tools without service interruption

Hi Galaxy team, Is there a way to add a tool without service interruption ? Something like a "sh run.sh --reload" (not "restart") command. I think I saw this information once, but I can't put my hand on it anymore. Thanks in advance ! F.T __

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

Hi, sorry for the late response ! I tested the modifications proposed in the "Allow to select multiple database" pull request and it works !!! Thanks a lot ! Floreline. P.S : I'm not familiar with all github functionnalities yet, but I will work on it ;) 2016-01-20 16:07 GMT+01:00 Peter Cock :

Re: [galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

I just have to add a tag "multiple=true" in the XML file but it seems a bit more complex. Am I missing something ? F.T 2016-01-20 10:33 GMT+01:00 Peter Cock : > On Wed, Jan 20, 2016 at 9:19 AM, Floreline TOUCHARD > wrote: > > Hi, > > > > I would like to

[galaxy-dev] EMBOSS 6.6.0 + NCBI-BLAST+ integration

Hi, I would like to add some tools of the EMBOSS suite (6.6.0) to my Galaxy instance. It seems that the only wrapper available for Galaxy is for the 5.0.0 version ( http://dev.list.galaxyproject.org/Galaxy-with-EMBOSS-5-or-EMBOSS-6-td4658043.html). I would like to know if someone has already trie

[galaxy-dev] logged in as 'user2' externally, but has a cookie as 'user1' invalidating session

Hi all, happy new year ! I finally manage to connect my Galaxy instance with my NIS service for external authentication but I have a few questions about it : - when I log in with another external account I get the following warning : "galaxy.web.framework.webapp WARNING 2016-01-05 11:52:24,741 Use

Re: [galaxy-dev] login problem (redirection to the login page)

the server side. Is there other cache than Firefox I should clear ? Thank, F.T Le 5 nov. 2015 18:16, "Floreline TOUCHARD" a écrit : > Hi, > > I come back to you with some news of my login problem. > I delete my browser cache and cookies with no result. > I restart all my se

Re: [galaxy-dev] login problem (redirection to the login page)

uld be aware of ? Is there another way to get an operational application ? And where did this issue come from ? I'm only testing the application but it surprises me since I had a working instance for few months. Thanks in advance, F.T 2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD : > Upd

Re: [galaxy-dev] login problem (redirection to the login page)

self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 303, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe 2015-11-04 15:09

Re: [galaxy-dev] login problem (redirection to the login page)

Here is some details : when I enable the access to Galaxy without authentication I'm redirected to the welcome page, but still I'm not connected (I can login/register) 2015-11-04 14:42 GMT+01:00 Floreline TOUCHARD : > Thanks for the "bidouille" ;) > > It didn'

Re: [galaxy-dev] login problem (redirection to the login page)

e" can help before you obtain a real solution to fix > this.. > > Cheers, > > Yvan > > -- > > *De: *"Floreline TOUCHARD" > *À: *galaxy-dev@lists.galaxyproject.org > *Envoyé: *Mercredi 4 Novembre 2015 14:00:24 > *Objet: *[

[galaxy-dev] login problem (redirection to the login page)

Hi, this is not the first time I encounter this problem : I change the authentication mode (external to internal). And since then I cannot login with any account. Each time I'm redirected to the login page. Yet I haven't any log error. I have the galaxy-master 15.07 version. I cleared the firefox

[galaxy-dev] toolshed and proxy

Hi, I've got an issue with the toolshed : I can't open it. I installed my galaxy instance on a server protected by a firewall and proxy. The toolshed url (https://toolshed.g2.bx.psu.edu) is open for this server. The wget command works (I can download the index.html file). Firefox is configured wit

Re: [galaxy-dev] external authentication - empty REMOTE_USER

nd I get a "galaxy.web.framework.webapp WARNING 2015-10-22 10:37:19,762 User logged in as '@example.fr' externally, but has a cookie as '@example.fr' invalidating session" in the paster.log. Is it a syntax problem in my galaxy.conf file ? F.T 2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD

Re: [galaxy-dev] external authentication - empty REMOTE_USER

Hi, thanks for the quick reply ! I did edit the remoteuser.py file and started the daemon again, but there's no change in the output in paster.log. Am I missing something ? F.T 2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD : > Hi, > > I've got an issue with my exte

Re: [galaxy-dev] external authentication - empty REMOTE_USER

to update the entire application at the moment. F. T Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" a écrit : > Hi, > > I've got an issue with my external authentication configuration. I use > Apache and the mod_perl > > modules (AuthenNIS + AuthzNIS + Net-NI

[galaxy-dev] external authentication - empty REMOTE_USER

Hi, I've got an issue with my external authentication configuration. I use Apache and the mod_perl modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS accounts. I have the authentication form when I try to access galaxy web page. But after a successful authentication it

[galaxy-dev] [Galaxy-dev] user authentication (NIS)

Hi, I read the doc about external authentication but I'm not sure to understand all of it (I'm a newbie). I would like to use both capacities of NIS : - the use of Linux login and password for access to Galaxy - and exploit the system user accounts to the restric