[galaxy-dev] Galaxy XML from python's argparse

2015-01-26 Thread Eric Rasche
reports/suggestions are welcome https://github.com/erasche/gxargparse/issues/! Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru

Re: [galaxy-dev] show stopper for my galaxy installation

2015-01-22 Thread Eric Rasche
by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche

Re: [galaxy-dev] Serving Galaxy at a sub directory - symptoms without filter-with = proxy-prefix

2015-02-25 Thread Eric Rasche
in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II

Re: [galaxy-dev] Issue writing functional tool test with repeat tag in config

2015-04-21 Thread Eric Rasche
to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM

Re: [galaxy-dev] Migrating user account from galaxy specific to LDAP

2015-04-30 Thread Eric Rasche
of the main reasons is being able to 'impersonate a user', a capability lost when using external authentication. We do not regret it ;) Cheers, Jelle On Thu, Apr 30, 2015 at 5:01 PM, Eric Rasche e...@tamu.edu wrote: Hi Teshome, I solved this by manually editing the user's emails in the database. I

Re: [galaxy-dev] Migrating user account from galaxy specific to LDAP

2015-04-30 Thread Eric Rasche
LDAP authentication to local user authentication to have a bit more control. One of the main reasons is being able to 'impersonate a user', a capability lost when using external authentication. We do not regret it ;) Cheers, Jelle On Thu, Apr 30, 2015 at 5:01 PM, Eric Rasche e...@tamu.edu

Re: [galaxy-dev] Migrating user account from galaxy specific to LDAP

2015-04-30 Thread Eric Rasche
subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio

Re: [galaxy-dev] substitution of special characters in arguments of galaxy tools

2015-04-16 Thread Eric Rasche
in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center

Re: [galaxy-dev] Installing workflows from the Tool Shed is very confusing

2015-04-07 Thread Eric Rasche
the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e

Re: [galaxy-dev] How to access the api by jQuery ajax?

2015-06-04 Thread Eric Rasche
I can't speak to your CORS issues, but you may have to add some custom CORS header in your webserver. If you have a webserver in front of Galaxy, it is absolutely for sure stripping REMOTE_USER out. If you're using remote_user authentication, you'll have to do something a bit different, and

[galaxy-dev] Fwd: Adding packages for bedtools and ucsc-utils for Trackster?

2015-06-18 Thread Eric Rasche
... have a look at https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse Developed by IUC member Eric Rasche. Cheers, Bjoern On 18.06.2015 10:00, Peter van Heusden wrote: I've tried that - I've added the Environment Modules for the relevant tools to the local_env.sh file, so

Re: [galaxy-dev] LDAP and new history creation

2015-06-26 Thread Eric Rasche
/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru

[galaxy-dev] Adding BioPython as a dependency to Galaxy

2015-05-20 Thread Eric Rasche
/clustal/etc), and leveraging BioPython for format conversion there. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru

[galaxy-dev] bcftools 1.2 wrappers

2015-08-11 Thread Eric Rasche
Howdy Tool Developers, I'm not seeing any wrappers for bcftools 1.2 in the toolsheds, figured I'd ask around in case someone else had progress on wrapping them. If not I'll generate wrappers this week. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas

Re: [galaxy-dev] API for job and workflow input metadata

2015-08-21 Thread Eric Rasche
://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-05 Thread Eric Rasche
/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] Call for Tool Shed Admins

2015-08-03 Thread Eric Rasche
, and currently are under heavy development. 2015-08-03 14:50 GMT-05:00 Eric Rasche e...@tamu.edu: yes please! :) (it's private though, and we're wavering on using it vs using a git repository of tools in $galaxy_root/tools/) 2015-08-03 14:03 GMT-05:00 Martin Čech mar...@bx.psu.edu: Hi everybody

Re: [galaxy-dev] Ipython behind apache proxy, firefox CORS error

2015-07-16 Thread Eric Rasche
=%2Fipython%2F${PORT}%2Ftree') With this, it's pretty close, however the containers aren't yet aware of the new URL they're to be accessed under: From 76bf20de305d64e544911a86ea5d0cb03e4281bd Mon Sep 17 00:00:00 2001 From: Eric Rasche e...@tamu.edu Date: Thu, 16 Jul 2015 12:00:47 -0500 Subject: [PATCH

Re: [galaxy-dev] Ipython behind apache proxy, firefox CORS error

2015-07-15 Thread Eric Rasche
in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center

Re: [galaxy-dev] JBrowse failed to install

2015-11-08 Thread Eric Rasche
ail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Eric Rasche Programmer

Re: [galaxy-dev] rgFastQC.py error - cannot find executable /fastqc

2015-11-16 Thread Eric Rasche
; 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing

Re: [galaxy-dev] Good entry bugs/entry points to start developing for Galaxy

2015-10-30 Thread Eric Rasche
Hi Damian, 30. okt. 2015 9.43 p.m. skrev Damian Birchler : > > Hi list > > I'm looking to get involved in Galaxy as a developer and I was wondering > whether you could point me to one (a few) bugs that you consider having > a go at would be a good entry point into

Re: [galaxy-dev] Good entry bugs/entry points to start developing for Galaxy

2015-10-30 Thread Eric Rasche
ent on the card! It's an easy way for us to keep in touch and whenever you solve the bug github can associate it with your pull request and close it :-) > > Cheers, > Damian > > On 2015-10-30 22:04, Eric Rasche wrote: > > Hi Damian, > > > > > >

Re: [galaxy-dev] IPython and Rstudio are missing

2015-11-06 Thread Eric Rasche
ther Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas

Re: [galaxy-dev] Galaxy Interactive Environment devs

2015-10-15 Thread Eric Rasche
tats and impressions from users! If people wouldn't be opposed to it, we could be something as simple as an admin-enabled, opt-in tracking pixel just to track/report notebook usage? Or maybe a "+1/-1" button at the top for "It was useful/it wasn't useful" but maybe t

Re: [galaxy-dev] User API keys with External (LDAP) authentication disabled?

2015-10-07 Thread Eric Rasche
by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/searc

Re: [galaxy-dev] User API keys with External (LDAP) authentication disabled?

2015-10-08 Thread Eric Rasche
/872.patch Ciao, Eric On 10/07/2015 04:43 PM, Eric Rasche wrote: > Not from the admin interface right now. I noted this bug just the other > day and intended to fix it as it applied to us as well. > Until then, you can easily change the API key manually in the database. > > Cheers, &

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

2015-10-21 Thread Eric Rasche
tic/robots.txt [L] >RewriteRule ^(.*) http://localhost:2209$1 [P] > > > > > > Thanks in advance ! > > F.T > > > > _______ > Please keep all replies on the list by using "reply all"

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
subscriptions to this > and other Galaxy lists, please use the > interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists u

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
rns a 301 if it's missing with the location of your login page) > > > On Tue, Oct 13, 2015 at 11:10 AM, Eric Rasche <e...@tamu.edu > <mailto:e...@tamu.edu>> wrote: > > Hi Ryan, > > On 10/13/2015 09:50 AM, Ryan G wrote: > > Hi all - In regards t

Re: [galaxy-dev] External User Authenticaion

2015-10-13 Thread Eric Rasche
gt; > Users never see http://galaxy.mycompany.com:8080they will always see > http://mycompay.com/galaxy > > > > On Tue, Oct 13, 2015 at 12:36 PM, Eric Rasche <e...@tamu.edu > <mailto:e...@tamu.edu>> wrote: > > > > On 10/13/2015 11:34 AM, R

Re: [galaxy-dev] Galaxy Interactive Environment devs

2015-10-13 Thread Eric Rasche
d it was unpleasant/complex to have your Galaxy user `sudo` or `sg` to run docker (https://github.com/galaxyproject/galaxy/pull/777) > > Cheers to Texas, > > Sebastian Grüße nach München, > > > Eric Rasche schrieb: >> Howdy y'all, >> >> I'm building s

Re: [galaxy-dev] Tool code for symlinking a data collection from input to output?

2015-11-17 Thread Eric Rasche
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: &g

[galaxy-dev] Galaxy Interactive Environment devs

2015-09-23 Thread Eric Rasche
containers, this won't be an issue for you, you'll just need to rebuild your containers once we release 15.10 versions. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A University College Station, TX 77843 404-692-2048 e...@tamu.edu

Re: [galaxy-dev] security: brute force login

2016-01-04 Thread Eric Rasche
l 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyp

Re: [galaxy-dev] Tool Release Announcement: JBrowse-in-Galaxy v0.4

2015-12-31 Thread Eric Rasche
not check it right now I am wondering if > it has SPARQL support? To visualise genetic content from a spraql end > point. > > > > Happy new year! > > > > > *From: *Eric Rasche <mailto:e...@tamu.edu> > *Sent: *31 December 2015 21:46 > *To: *N: <m

[galaxy-dev] Tool Release Announcement: JBrowse-in-Galaxy v0.4

2015-12-31 Thread Eric Rasche
interstitial, open JBrowse in the main panel with one click. * Support for translation tables other than table 1. More details in the pull request <https://github.com/galaxyproject/tools-iuc/pull/507> for the curious. And a silly image to top it off :) Ciao, Eric -- Eric Rasche Programmer II

Re: [galaxy-dev] RFC: new

2016-01-04 Thread Eric Rasche
res. * may someday offer advanced features like dependency tree building The Cargo Port * Packages from any upstream * Pretty much feature complete > > https://bioarchive.galaxyproject.org/ > > Peter > > > ___ > Pleas

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Eric Rasche
> ProxyPass/ http://localhost:8080 > ProxyPassReverse / http://localhost:8080 > > / > Did I modify the above files correctly?/ > > / > /Thank you in advance, > > / > /Mic > / > > > > On Tue, Dec 22,

Re: [galaxy-dev] IE Apache Proxy config file

2015-12-19 Thread Eric Rasche
19. des. 2015 5.30 a.m. skrev "Mic" : > > Hello, > I would like to setup Rstudio and IPython using Apache Proxy. I found the following settings: > > # IPython specific. Other IEs may require their own routes. > ProxyPass/galaxy/gie_proxy/ipython/api/kernels

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread Eric Rasche
n advance. > > Mic > > > > On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <e...@tamu.edu> wrote: >> >> Hi Mic, >> >> Since you asked for the supervisord config... it would look something >> like this:] >> >> [program:galaxy_proxy] &

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread Eric Rasche
> ___ > 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: > https://lists.galaxyproject.org/ >

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

2015-11-23 Thread Eric Rasche
alaxyproject.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 &g

Re: [galaxy-dev] Does anybody know if ts (a task scheduler) is supported under Galaxy.

2015-11-24 Thread Eric Rasche
_ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy m

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

2015-11-30 Thread Eric Rasche
roject.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

Re: [galaxy-dev] Alternative methods for external authentication

2016-03-01 Thread Eric Rasche
riptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- -- Eric Rasche Programmer II Center for Phage Techn

Re: [galaxy-dev] backslash in string for galaxy tool

2016-03-10 Thread Eric Rasche
o this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Te

Re: [galaxy-dev] Scaling tools: data available?

2016-03-14 Thread Eric Rasche
> server, I'm just trying to understand how you envision these metrics > getting into the GRT? > > Peter > > On 22 February 2016 at 07:31, Eric Rasche <e...@tamu.edu> wrote: > >> Hi peter, >> >> I've been working on this in the past but got caught up in othe

Re: [galaxy-dev] Password Parameter Opinions

2016-07-28 Thread Eric Rasche
ep 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http:/

Re: [galaxy-dev] Deprecated code file tag

2016-08-03 Thread Eric Rasche
ions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A,

Re: [galaxy-dev] Galaxy URL and api key tool config

2016-08-03 Thread Eric Rasche
alaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A University College Station, TX 77843 404-692-2048 e...@tamu.edu <mailto:e...@tamu.edu> Not responding quickly enough

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

2016-08-08 Thread Eric Rasche
ttps://urldefense.proofpoint.com/v2/url?u=http-3A__lcsb.uni.lu_=CwMF-g=ODFT-G5SujMiGrKuoJJjVg=p9uZby14OqW9zcjBSjiDKw=pwYDgdauhpWnUSnnqVAB6Xyn2OzpGsIMkWdC8fyNRu0=Ll-0NRWHk-0Kb159GLi8cgxakoFwK4BQyp39IRY0S48=> > - > This message is confidential and may contain privileged information. > It is i

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

2016-08-08 Thread Eric Rasche
iDKw=VV-vUll4GtQX9nsboaQbXHu4z31_SAdpkA-8nu-bzUk=bJ6NwuiRobXf-sPXjKoJ3KtEQaDOvG_ViZwLwKKumv8=> >> - >> This message is confidential and may contain privileged information. >> It is intended for the named recipient only. If you receive it in >> error please notify me

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

2016-08-08 Thread Eric Rasche
e interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, Biochemistry & Biophysics Texas A University College Stat

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

2016-08-08 Thread Eric Rasche
.di...@uni.lu <mailto:sarah.di...@uni.lu> http://lcsb.uni.lu > <https://urldefense.proofpoint.com/v2/url?u=http-3A__lcsb.uni.lu_=CwMF-g=ODFT-G5SujMiGrKuoJJjVg=p9uZby14OqW9zcjBSjiDKw=8xM31HcPZ4Ec33URP78V75DF81DjSEDfXNB5w7ccyCk=eJz9GaBHRiG29dlQUEpFrrop4cIl-Wc7LK0GRRCeSPA=> > - > Thi

Re: [galaxy-dev] Error running JBrowse

2016-08-16 Thread Eric Rasche
__ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use t

[galaxy-dev] Testing workflows

2016-12-13 Thread Eric Rasche
Wondering if anyone has tooling to test a workflow as it exists in a specific galaxy instance? I'm looking to test some of my user's manually built workflows in our galaxy instance to make sure that we can detect issues when they arise (e.g. due to changes in the interfaces of our non-toolshed

[galaxy-dev] galaxy & DFARS

2017-06-02 Thread Eric Rasche
Has anyone dealt with DFARS requirements and data in Galaxy? Similar themes across other requirement sets might be: encryption of data at rest, DoD 32-pass secure deletion of data, providing access logs for datasets/histories/intermediate steps, providing logs of changes to access control