Re: [galaxy-dev] Connecting LDAP with Galaxy

Great, thanks Nicola! Am 08.08.2016 um 23:53 schrieb Nicola Soranzo: > There is one already: https://github.com/galaxyproject/galaxy/issues/2593 > > I may take a stab at it in the next days. > > Cheers, > Nicola > > Björn Grüning ha scritto > >> >> >> Am 08.08.2016 um 20:14

Re: [galaxy-dev] Connecting LDAP with Galaxy

There is one already: https://github.com/galaxyproject/galaxy/issues/2593 I may take a stab at it in the next days. Cheers, Nicola Björn Grüning ha scritto > > >Am 08.08.2016 um 20:14 schrieb Tiago Antao: >> I was reading a bit about this (I manage a LDAP server, but I am far >>

Re: [galaxy-dev] Connecting LDAP with Galaxy

Am 08.08.2016 um 20:14 schrieb Tiago Antao: > I was reading a bit about this (I manage a LDAP server, but I am far > from a specialist) and the format is actually too flexible: Any UTF-8 > encoding with up to 64 characters. > > I suspect basic punctation marks would be enough. Though I could

Re: [galaxy-dev] External user auth and API

Hi Sarah, On 08. aug. 2016 13:58, Sarah DIEHL wrote: > Hi Eric, > > thanks for the hint regarding uWSGI. What doesn't work is importing > files from the local disk (of the galaxy server) to the data library > (see attached screenshot). Everything else seems to be fine, I haven't > encountered any

Re: [galaxy-dev] Connecting LDAP with Galaxy

I don't think there is any good reason. Public username's main purpose originally was to generate slugs for URLs so we left out "-". Shouldn't break anything to add it. On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning wrote: > Does anyone know why we have this

Re: [galaxy-dev] Connecting LDAP with Galaxy

Does anyone know why we have this restriction? Can we change it? Am 08.08.2016 um 17:31 schrieb Tiago Antao: > Sorry, that was what I meant and explained myself poorly. > > This is actually a very serious problem if one wants to integrate Galaxy > in an existing SSO environment based on LDAP. >

Re: [galaxy-dev] Connecting LDAP with Galaxy

Sorry, that was what I meant and explained myself poorly. This is actually a very serious problem if one wants to integrate Galaxy in an existing SSO environment based on LDAP. Tiago On 2016-08-08 09:28, Nicola Soranzo wrote: Actually it's Galaxy (not the LDAP integration) that doesn't

Re: [galaxy-dev] Connecting LDAP with Galaxy

Actually it's Galaxy (not the LDAP integration) that doesn't allow underscores in usernames, in fact if you try to register a new user on e.g. usegalaxy.org and the username has an underscore, you'll get this error: Public name must contain only lowercase letters, numbers and "-". It also

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning wrote: > Hi Peter, > > Am 08.08.2016 um 15:54 schrieb Peter Cock: >> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche wrote: >>> Hi Peter, >>> >>> The cargo port is the ideal place for this, however it does not

Re: [galaxy-dev] view details not working

Hi Nicola, It's suppose to be the 16.04. commit b79474083b08860923f7f28fc1e7442b53f925db Merge: 7c94ac8 5aefe1b Author: Martin Cech Date: Wed Apr 20 15:22:20 2016 -0400 Merge pull request #2206 from dannon/master Sanity check of master update. Le 08/08/2016

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

Peter: depot is something we plan on maintaining and providing as a service as long as Galaxy. The cargo-port we will also expand in future (eg to provide dynamic fallback at installation time. It is the right place to put your mira backups (and any other packages you care about in recipes).

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

Hi Peter, Am 08.08.2016 um 15:54 schrieb Peter Cock: > On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche wrote: >> Hi Peter, >> >> The cargo port is the ideal place for this, however it does not support >> manual uploads of files. >> > > Thanks Eric, > > You mean

Re: [galaxy-dev] view details not working

Hi Vincent, what release of Galaxy are you using? It should be fixed by https://github.com/galaxyproject/galaxy/pull/2312 , which is available in latest release_16.01 and following. Cheers, Nicola On 08/08/16 14:58, Vincent Cahais wrote: Dear all, I have a very strange bug on my galaxy

[galaxy-dev] view details not working

Dear all, I have a very strange bug on my galaxy server. The view details button is not working anymore for the new datasets. I get an Internal server Error. It's still working for older datasets, it's only an issue for the new one, independently of the tool. Best regards Vincent

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche wrote: > Hi Peter, > > The cargo port is the ideal place for this, however it does not support > manual uploads of files. > Thanks Eric, You mean https://github.com/galaxyproject/cargo-port Is that something which might be addressed in

Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

Hi Peter, The cargo port is the ideal place for this, however it does not support manual uploads of files. On 08. aug. 2016 13:37, Peter Cock wrote: > Hello all, > > How do tool wrapper developers/packagers go about adding entries > to the Galaxy depot? There isn't a GitHub repository for this

[galaxy-dev] Adding packages to depot.galaxyproject.org

Hello all, How do tool wrapper developers/packagers go about adding entries to the Galaxy depot? There isn't a GitHub repository for this is there? Specifically I want to upload some older MIRA releases, e.g. these URLs have broken, but I have the original files and checksums:

Re: [galaxy-dev] External user auth and API

Hi Sarah, On 08. aug. 2016 07:44, Sarah DIEHL wrote: > Dear all, > > since no one replied so far to the main problem I had and it might > have gotten lost in the conversation, I ask again: Does somebody know > how to configure external user auth with apache such that API (from > external, e.g.

Re: [galaxy-dev] conversion issue

I tried to reinstall some tools, but I still get an error message: Fatal error: Exit code 1 () bedtools: /galaxy-central/tool_deps/ucsc_tools/312/iuc/package_ucsc_tools_312/2d6bafd63401/lib/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by bedtools) needLargeMem: trying to

[galaxy-dev] External user auth and API

Dear all, since no one replied so far to the main problem I had and it might have gotten lost in the conversation, I ask again: Does somebody know how to configure external user auth with apache such that API (from external, e.g. bioblend) and dataset import in the data libraries work? When I