Re: [galaxy-dev] Remote User Logout
Hi,
I'm currently using one of those hacks, and it seems to work nicely for
the user (Chrome + FF at least) but it does need some messy setting up
in Apache and some cunning redirects in place. I've pasted the relevant
file fragments below. It's somewhat confounded with my stuff to enable
SFTP uploads but hopefully you get the idea and the original explanation
on Stackoverflow is pretty good. The remote_user_logout_href is
something I got to by trial and error.
Cheers,
TIM
===
% cat /usr/share/galaxy-server/logout/.htaccess
# HaCk based on
http://stackoverflow.com/questions/4163122/http-basic-authentication-log-out
# Authname must match the one in ../proxy/.htaccess
AuthType Basic
AuthName Galaxy_Server
AuthUserFile /usr/share/galaxy-server/logout/.htpasswd
Require user logout
===
% cat /usr/share/galaxy-server/logout/.htpasswd
#Password is logout. This in not a secret.
logout:$apr1$0eB1iURY$kwqa0c8tXksbjPQLYqr6s.
===
% cat /usr/share/galaxy-server/proxy/.htaccess
# Security settings for Galaxy proxied via Apache. Note the actual
# proxy config is under /etc/apache2/conf.d/galaxy. If for some
# reason you wanted Apache proxy with internal Galaxy authentication
# then you could remove this file and Apache would no longer insist on
# authentication.
AuthBasicProvider external
AuthExternal pwauth
AuthType Basic
AuthName Galaxy_Server
#I'd like to do this, but it upsets Firefox. Use ErrorDocument instead.
# AuthName Galaxy Server: \
# Log in with regular username and password. \
# Users need to be in the galaxy system group.
ErrorDocument 401 html\
title401 Authorization Required/title\
h1Log-in to Galaxy failed/h1\
pYou should have been prompted to log into the Galaxy server. \
You need to give your regular system username and password. \
Please reload this page to try again./p\
pIf this fails, check that you are a member of the galaxy system
group, by \
running codegroups/code on the command line./p\
pTo add a user, eg. user1, to this group, you may use the
command:/p\
ullicodesudo usermod -aG galaxy user1/code/ul/li\
/html
# You may want to comment these 2 lines out or to
# change the group required, but users still need to
# be in the galaxy group for SFTP uploads to work properly.
AuthzUnixgroup on
Require group galaxy
# This is needed to tell Galaxy about the remote
# user.
RequestHeader set REMOTE_USER %{RU}e env=RU
RequestHeader unset Authorization env=RU
===
% cat /etc/galaxy-server/universe_wsgi.d/31_apache-proxy.ini
# Settings added by debian-galaxy-apache-proxy to switch Galaxy over to
# authenticating by real user accounts and also permitting uploads.
[app:main]
# Other scripts assume that maildomain is localhsot, so you can't just
# change the setting below and expect everythig to work.
use_remote_user = True
remote_user_maildomain = localhost
# Users may copy files here directly or upload via SFTP/SCP
ftp_upload_dir = /var/lib/galaxy-server/transfer
ftp_upload_site = *** Transfer files via SCP or SFTP to
/var/lib/galaxy-server/transfer/... ***
# There is no neat way to log out a user with Basic Auth, but here is a
non-neat way.
# Not yet tested on IE.
remote_user_logout_href = javascript:var r=new
XMLHttpRequest();r.onreadystatechange=function(){if(r.readyState==4)window.location.replace('logout.html')};r.open('get','logout.html',true,'logout','logout');r.send();
===
--
Tim Booth tbo...@ceh.ac.uk
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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Re: [galaxy-dev] Fwd: Galaxy tool is not running
Hi Eric, Thanks for reporting this error, it has been resolved in changeset 12278:04bce95d8fd2 and 12281:6c5913a4b701. Please let us know if you encounter additional issues. Thanks for using Galaxy, Dan On Jan 27, 2014, at 4:56 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hi Greg or James, This morning I got a question about the Aggregate Datapoints tool which only returned nan results. in line 204@aggregate_scores_in_intervals.py I found out that the if not isNaN( score ): should be if not isnan( score ): on https://usegalaxy.org/tool_runner?tool_id=aggregate_scores_in_intervals2 the tool also seems to be failing. I hope you could use this, Eric -- Forwarded message -- From: Sandra Gavaldá Martín Date: 26 January 2014 20:52 Subject: Galaxy tool is not running To: Kuijt, Eric eric.ku...@wur.nl Hello Eric, My name is Sandra Gavaldá and I am very grateful for Galaxy tools. I usually use the one Aggregate datapoints for fusioning files with intervals and my .wig files. I noticed you made some updating and I do not why I can not obtain any result now. -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.ku...@wur.nl Web: http://www.cvi.wur.nl Screen Shot 2014-01-26 at 20.46.50.pngScreen Shot 2014-01-26 at 20.50.08.png___ 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] Help with two questions about transfering data to galaxy local instance
I don't know of a way to accomplish what you are describing with the tool framework - without prepopulating static files with all of the data you will need - and even then I am not exactly sure what to do. But it sounds like you would like to fetch this data from a database or web service of some kind dynamically - so that doesn't sound like a good path. More details however would help formulate a better response. My guess is a tool is not an ideal abstraction that you should be using right here - you could write a local extension to Galaxy to do this or you can write a data source and corresponding data source tool (https://wiki.galaxyproject.org/Admin/Internals/Data%20Sources). Though some people have done really creative things with the tool framework so I could be totally wrong, hopefully if someone else has an idea they will speak up. If you want to write a local extension to Galaxy you can look at some the controllers in lib/galaxy/webapps/galaxy/controllers/ and write your own that would have actions for displaying a form to collect the data and update the page with details, as well as one to perform the import, and you will need to write mako templates to describe your pages (in templates/webapps/galaxy). You could do the import using the existing structures in Galaxy or target the API. Regardless this will be a lot of work. Another possibility is to drive this entire process from an external webapp either existing (is something being used to manage this data you targeting) or a new one in whatever web programming environment you are most comfortable with. In response to how to transfer files to your local Galaxy instance faster - I would need to know where you are getting them from and what method you are currently using to copy them. I hope this helps. -John On Thu, Jan 23, 2014 at 8:35 PM, Huayan Gao huayan...@gmail.com wrote: Hi, I am doing a data transferring interface in galaxy. I want to accomplish two things. First, when user enters a number, the interface will show some related information or search results (eg, related files) by this unique number. Then user can select the files they wanted to put into galaxy history panel for further data analysis. So my question is, can add a button in xml interface or python code to show the search results? The second question is that the files could be big. How can I transfer the files faster to my local galaxy instance? The current copy is just too slow. Thanks! ___ 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] Remote User Logout
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi Tim,
Amazing! Thank you for sharing that code. That'll save me some work when
I get around to implementing it on my galaxies. I'll add a Wiki page for
it later today, lest this knowledge be lost to the mailing list.
Cheers,
Eric
On 01/27/2014 06:27 AM, Tim Booth wrote:
Hi,
I'm currently using one of those hacks, and it seems to work nicely for
the user (Chrome + FF at least) but it does need some messy setting up
in Apache and some cunning redirects in place. I've pasted the relevant
file fragments below. It's somewhat confounded with my stuff to enable
SFTP uploads but hopefully you get the idea and the original explanation
on Stackoverflow is pretty good. The remote_user_logout_href is
something I got to by trial and error.
Cheers,
TIM
===
% cat /usr/share/galaxy-server/logout/.htaccess
# HaCk based on
http://stackoverflow.com/questions/4163122/http-basic-authentication-log-out
# Authname must match the one in ../proxy/.htaccess
AuthType Basic
AuthName Galaxy_Server
AuthUserFile /usr/share/galaxy-server/logout/.htpasswd
Require user logout
===
% cat /usr/share/galaxy-server/logout/.htpasswd
#Password is logout. This in not a secret.
logout:$apr1$0eB1iURY$kwqa0c8tXksbjPQLYqr6s.
===
% cat /usr/share/galaxy-server/proxy/.htaccess
# Security settings for Galaxy proxied via Apache. Note the actual
# proxy config is under /etc/apache2/conf.d/galaxy. If for some
# reason you wanted Apache proxy with internal Galaxy authentication
# then you could remove this file and Apache would no longer insist on
# authentication.
AuthBasicProvider external
AuthExternal pwauth
AuthType Basic
AuthName Galaxy_Server
#I'd like to do this, but it upsets Firefox. Use ErrorDocument instead.
# AuthName Galaxy Server: \
# Log in with regular username and password. \
# Users need to be in the galaxy system group.
ErrorDocument 401 html\
title401 Authorization Required/title\
h1Log-in to Galaxy failed/h1\
pYou should have been prompted to log into the Galaxy server. \
You need to give your regular system username and password. \
Please reload this page to try again./p\
pIf this fails, check that you are a member of the galaxy system
group, by \
running codegroups/code on the command line./p\
pTo add a user, eg. user1, to this group, you may use the
command:/p\
ullicodesudo usermod -aG galaxy user1/code/ul/li\
/html
# You may want to comment these 2 lines out or to
# change the group required, but users still need to
# be in the galaxy group for SFTP uploads to work properly.
AuthzUnixgroup on
Require group galaxy
# This is needed to tell Galaxy about the remote
# user.
RequestHeader set REMOTE_USER %{RU}e env=RU
RequestHeader unset Authorization env=RU
===
% cat /etc/galaxy-server/universe_wsgi.d/31_apache-proxy.ini
# Settings added by debian-galaxy-apache-proxy to switch Galaxy over to
# authenticating by real user accounts and also permitting uploads.
[app:main]
# Other scripts assume that maildomain is localhsot, so you can't just
# change the setting below and expect everythig to work.
use_remote_user = True
remote_user_maildomain = localhost
# Users may copy files here directly or upload via SFTP/SCP
ftp_upload_dir = /var/lib/galaxy-server/transfer
ftp_upload_site = *** Transfer files via SCP or SFTP to
/var/lib/galaxy-server/transfer/... ***
# There is no neat way to log out a user with Basic Auth, but here is a
non-neat way.
# Not yet tested on IE.
remote_user_logout_href = javascript:var r=new
XMLHttpRequest();r.onreadystatechange=function(){if(r.readyState==4)window.location.replace('logout.html')};r.open('get','logout.html',true,'logout','logout');r.send();
===
- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas AM University
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[galaxy-dev] galaxy tries to access toolshed at http instead of using https
dear all, When I try to install a tool from our local toolshed Galaxy changes the repository url from HTTPS to HTTP and throws an error. I'm setting up a local (intranet) toolshed for some of our in house tools. We run galaxy (latest stable) on HTTPS://nioo0025.nioo.int/galaxy The toolshed is setup at HTTPS://nioo0025.nioo.int/toolshed My tool_sheds_conf.xml contains: (note the HTTPS protocol) ?xml version=1.0? tool_sheds tool_shed name=Galaxy main tool shed url=http://toolshed.g2.bx.psu.edu// tool_shed name=Galaxy test tool shed url=http://testtoolshed.g2.bx.psu.edu// tool_shed name=NIOO Galaxy tool shed url=https://nioo0025.nioo.int/toolshed// /tool_sheds So far so good. The toolshed works and I can upload tool tarballs I created. Galaxy sees the toolshed and the uploaded tool. When I try to install the tool I get the following message: paster.log:tool_shed.tool_shed_registry DEBUG 2014-01-27 16:00:13,485 Invalid url 'http://nioo0025.nioo.int/toolshed/' received by tool shed registry's password_manager_for_url method. paster.log:10.128.34.21 - - [27/Jan/2014:16:00:13 +0200] GET /galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://nioo0025.nioo.int/toolshed/repository_ids=6c73c198d6105528changeset_revisions=d4127427fd4c HTTP/1.1 500 - - Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0 basically telling me that our Galaxy instance tries to access the toolshed repo via HTTP instead of HTTPS. How can I instruct Galaxy to use the https location of the toolshed as specified in tool_sheds_conf.xml? Thanks for any help Victor ___ 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] HTML form of select parameter
I have attached a patch to disable this. The swap over happens when
the number of items gets sufficiently large and a jQuery-based widget
called select2 replaces all select boxes in Galaxy - unless explicitly
disabled. I understand the desire to disable this. I am not sure
anyone is really very pleased with select2 for multiple select widgets
- it might be worth just disabling it for multiple select form
elements all together globally. I don't know.
-John
On Thu, Jan 23, 2014 at 4:23 AM, Johannes Eichner
johannes.eich...@uni-tuebingen.de wrote:
Dear Galaxy Dev-Team,
when using the select parameter in conjunction with options loaded from
a text file in the tool_data_path directory (e.g., options
from_file=available_options.txt) and with the multiple attribute set
to true, I found that the form of the corresponding HTML widget
displayed in the webinterface depends on the number of options listed in
the text file. Is there a way to avoid this behaviour in the sense that
a fixed HTML form is used independent of the number of available
options? It would be great if this was possible, for instance, by
changing the value of the display attribute of the select parameter.
However, I would also be glad if you could just tell me, where this
behaviour of Galaxy is implemented in the source code, such that I can
change it according to my needs.
Kind regards,
Johannes
--
Dipl.-Inf. (Bioinf.) Johannes Eichner
Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 / 29 78970 Fax: (+49/0) 7071 / 29 5091
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diff --git a/templates/webapps/galaxy/tool_form.mako b/templates/webapps/galaxy/tool_form.mako
index 8d67b10..0039066 100644
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -106,6 +106,9 @@
}
});
});
+
+$('select[multiple]').select2(destroy);
+
});
%if not add_frame.debug:
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[galaxy-dev] Galaxy problem with DRMAA
Hi everybody, I managed to configure Galaxy to work with DRMAA in our cluster but after the job finished, the dataset state is set to error. Here is the last few lines of the paster.log file: galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:50,449 (181) submitting with credentials: jing [uid: 3663] galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:50,490 (181) Job script for external submission is: /work/galaxy/galaxy/galaxy-dist/database/pbs/181.jt_json galaxy.jobs.runners.drmaa INFO 2014-01-27 10:52:51,175 (181) queued as 961147 galaxy.jobs DEBUG 2014-01-27 10:52:51,225 (181) Persisting job destination (destination id: drmaa) galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:51,781 (181/961147) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2014-01-27 10:52:56,004 (181/961147) state change: job finished normally galaxy.jobs DEBUG 2014-01-27 10:52:56,276 (181) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /work/galaxy/galaxy/galaxy-dist/database/job_working_directory/000/181 galaxy 11295 galaxy.jobs DEBUG 2014-01-27 10:52:57,161 (181) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /work/galaxy/galaxy/galaxy-dist/database/job_working_directory/000/181 galaxy 11295 galaxy.jobs DEBUG 2014-01-27 10:52:59,777 setting dataset state to ERROR galaxy.jobs DEBUG 2014-01-27 10:52:59,871 job 181 ended In the browser, the stderr file says: Traceback (most recent call last): File /work/galaxy/galaxy/galaxy-dist/tools/data_source/data_source.py, line 6, in module from galaxy.util.json import from_json_string, to_json_string File /work/galaxy/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 14, in module pkg_resources.require( 'docutils' ) File /work/galaxy/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 414, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['docutils'] Traceback (most recent call last): File ./scripts/set_metadata.py, line 29, in module import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /work/galaxy/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line 10, in module eggs.require(pexpect) File /work/galaxy/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py, line 414, in require raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) ) galaxy.eggs.EggNotFetchable: ['pexpect']? The docutils and pexpect eggs are in the /work/galaxy/galaxy/galaxy-dist/eggs folder and I don't see why they are not fetchable. Any help is appreciated. Thanks. -Jing ___ 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] Remote User Logout
Hi Eric, Tim, Hi Tim, Amazing! Thank you for sharing that code. That'll save me some work when I get around to implementing it on my galaxies. I'll add a Wiki page for it later today, lest this knowledge be lost to the mailing list. That is an excellent suggestion. I've created a log board entry for it.: https://wiki.galaxyproject.org/Community/Logs The first for 2014. Feel free to edit, or send me revisions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] ProFFTPd-1.3.4d no longer able to authenticate users from Postgresql database
So I tried a new version of ProFTPd I was not able to locate lines in universe_wsgi.ini which disable PBKDF2 Lines from SQLLogFile.txt 2014-01-21 18:09:33,191 mod_sql/4.3[2275]: checking password using SQLAuthType 'sha1' 2014-01-21 18:09:33,191 mod_sql/4.3[2275]: 'sha1' SQLAuthType handler reports failure 2014-01-21 18:09:33,191 mod_sql/4.3[2275]: checking password using SQLAuthType 'sha256' 2014-01-21 18:09:33,191 mod_sql/4.3[2275]: 'sha256' SQLAuthType handler reports failure 2014-01-21 18:09:33,191 mod_sql/4.3[2275]: checking password using SQLAuthType 'pbkdf2' 2014-01-21 18:09:33,193 mod_sql/4.3[2275]: 'pbkdf2' SQLAuthType handler reports failure 2014-01-21 18:09:33,193 mod_sql/4.3[2275]: cmd_check 2014-01-21 18:09:33,193 mod_sql/4.3[2275]: cmd_auth 2014-01-21 18:13:54,383 mod_sql/4.3[2275]: entering postgres cmd_exit Proftpd.conf # Set up mod_sql to authenticate against the Galaxy database SQLEngine on SQLBackend postgres SQLConnectInfo galaxy_prod@:1234 user password SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1000 24 SQLAuthenticate users Launch interactive session to test /ProFTPd-1.3.5rc3/sbin/proftpd -d9 -n Std_Out shows: opening scoreboard '/shared/app/ProFTPd-1.3.5rc3/var/proftpd.scoreboard' RELINQUISH PRIVS at mod_auth.c:132 connected - local : :::128.23.191.200:21 connected - remote : 128.23.163.166:54865 FTP session opened. dispatching PRE_CMD command 'USER gal...@musc.edu' to mod_core dispatching PRE_CMD command 'USER gal...@musc.edu' to mod_core dispatching PRE_CMD command 'USER gal...@musc.edu' to mod_delay dispatching PRE_CMD command 'USER gal...@musc.edu' to mod_auth dispatching CMD command 'USER gal...@musc.edu' to mod_auth dispatching POST_CMD command 'USER gal...@musc.edu' to mod_sql dispatching POST_CMD command 'USER gal...@musc.edu' to mod_delay dispatching LOG_CMD command 'USER gal...@musc.edu' to mod_sql dispatching LOG_CMD command 'USER gal...@musc.edu' to mod_lo dispatching PRE_CMD command 'PASS (hidden)' to mod_core dispatching PRE_CMD command 'PASS (hidden)' to mod_core dispatching PRE_CMD command 'PASS (hidden)' to mod_sql_passwd dispatching PRE_CMD command 'PASS (hidden)' to mod_sql dispatching PRE_CMD command 'PASS (hidden)' to mod_delay dispatching PRE_CMD command 'PASS (hidden)' to mod_auth dispatching CMD command 'PASS (hidden)' to mod_auth no supplemental groups found for user 'gal...@musc.edu' ROOT PRIVS at mod_auth_pam.c:338 RELINQUISH PRIVS at mod_auth_pam.c:508 mod_sql_passwd/0.6: expected 'PBKDF2$sha256$1$vHKjTtvJsQSB2BuH$dGmwtBwxQ9yAz5kxzn9nF704PKeMnReV', got '1fd439fa1297e68426765a5c0b80a6ca4591888a' mod_sql_passwd/0.6: expected 'PBKDF2$sha256$1$vHKjTtvJsQSB2BuH$dGmwtBwxQ9yAz5kxzn9nF704PKeMnReV', got '268f784ba4c2283244e9730500f2a8126c84169ef985a70313c16464358ecc5c' mod_sql_passwd/0.6: expected 'PBKDF2$sha256$1$vHKjTtvJsQSB2BuH$dGmwtBwxQ9yAz5kxzn9nF704PKeMnReV', got '5f40c627d580e898f9742508c3aa0f0fbe87850e3b389ac1' USER gal...@musc.edu (Login failed): No such user found. I upgraded to ProFTPd-1.3.5rc3 because v 1.3.4 could not authenticate users on my local Galaxy instance. I understood that Galaxy was using SHA1 SHA256 PBKDF2 authentication but the programs are not yet compatible I used a proftpd conf file based on http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td4660295 .html I get the same problems when I use the following line in profited.conf SQLPasswordPBKDF2SHA256 1 24 Why am I seeing this mismatch? I tried to create a new user to see if the extant user accounts had somehow been left over from a previous build of the Galaxy user files, but the new user had the same issues. Puzzled Starr On 1/8/14, 5:26 PM, Hazard, E. Starr haza...@musc.edu wrote: Well when I declare SQLAuthTypesSHA1 SHA256 PBKDF2 SQLPasswordPBKDF2 SHA256 1 24 (per I get this response /shared/app/ProFFTPd-1.3.4d/sbin/proftpd -d9 -n hpcc3 proftpd[31522]: using TCP receive buffer size of 87380 bytes hpcc3 proftpd[31522]: using TCP send buffer size of 16384 bytes hpcc3 proftpd[31522]: mod_sql_passwd/0.4: registered 'md5' SQLAuthType handler hpcc3 proftpd[31522]: mod_sql_passwd/0.4: registered 'sha1' SQLAuthType handler hpcc3 proftpd[31522]: mod_sql_passwd/0.4: registered 'sha256' SQLAuthType handler hpcc3 proftpd[31522]: mod_sql_passwd/0.4: registered 'sha512' SQLAuthType handler hpcc3 proftpd[31522]: disabling runtime support for IPv6 connections hpcc3 proftpd[31522]: Fatal: SQLAuthTypes: unknown SQLAuthType 'PBKDF2' on line 106 of '/shared/app/ProFFTPd-1.3.4d/etc/proftpd.conf¹ SO ProFTPd-1.3.4d does not do PBKDF2 Just saw this post http://dev.list.galaxyproject.org/ProFTPD-integration-with-Galaxy-td466029 5 .html Will move to the release candidate version of ProFTPD And try that THANKS for responding Starr On 1/8/14, 5:05 PM,
[galaxy-dev] The main Galaxy Tool Shed is now running the next-stable branch
The main Galaxy Tool Shed is now running the next-stable branch in preparation for the next Galaxy release tentatively scheduled for 2 weeks from today. The current changeset revision on the main Tool Shed is: changeset: 12285:3fdf673bdfc9 branch: next-stable Complete documentation for all of the new Tool Shed features will be available for the release in 2 weeks, but feel free to check them out now if you want. Here are some of the more prominent new features: 1) The main Tool Shed is now scheduled to run the daily Tool Shed install and test framework, so installation and test results should hopefully be available for most repositories tomorrow. 2) Exporting and importing repository capsules should now be working between tool sheds (e.g., your local Tool Shed and the test Tool Shed, the test Tool Shed and the main Tool Shed, etc.). 3) Repository owners can now authorize others (either users or groups) to administer their repository using the new Manage repository administrators option in the Repository Actions pop-up menu. Please report any issues you uncover and we'll get them handled in preparation for the upcoming release. Thanks! Greg Von Kuster ___ 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] Install tools from Toolshed
Hello Shivani, The problem is either related to 3rd party cookies being enabled or a missing configuration in the universe.wsgi.ini file. This thread, in the second part, provides the full solution: http://dev.list.galaxyproject.org/Invalid-Galaxy-URL-None-Installing-Tools-Shed-td4659659.html Also, make sure you are running the latest version of Galaxy and followed the required upgrade procedures before trying. https://wiki.galaxyproject.org/DevNewsBriefs/ I am moving this over to the galaxy-...@bx.psu.edu mailing list, in case more follow-up is needed. That is the best list to use for troubleshooting local install / tool shed questions. Take care, Jen Galaxy team On 1/25/14 12:36 PM, Malik, Shivani wrote: HI, I am trying to install Deseq from the toolshed. I get the message:Repository installation is not possible due to an invalid Galaxy URL: *None*. You may need to enable cookies in your browser. I have enabled the cookies and tried both on Firefox and Chrome but could not get it to work. Can you help me on this? Thanks Shivani ___ 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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] Remote User Logout
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I figured this was as good of a time as any... I moved the AD/LDAP/External authentication out of the Apache Proxy page (who would think to look there?) and into its own page. I added my organisation's information on mod_auth_kerb while I was at it. That seemed like a reasonable place to put this sort of information. I've also reduced the solution to just the necessary portions, but it would need to be tested by someone. https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases#Logging_out_Basic_Auth.27d_Users I suggest we re-link the community log page to that subsection as it has more related information, if that is amenable to everyone. On 01/27/2014 11:47 AM, Dave Clements wrote: Hi Eric, Tim, Hi Tim, Amazing! Thank you for sharing that code. That'll save me some work when I get around to implementing it on my galaxies. I'll add a Wiki page for it later today, lest this knowledge be lost to the mailing list. That is an excellent suggestion. I've created a log board entry for it.: https://wiki.galaxyproject.org/Community/Logs The first for 2014. Feel free to edit, or send me revisions. Thanks, Dave C. Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.edu -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJS5rnVAAoJEMqDXdrsMcpVG+oQAIdCRLGJKMvgsb9kVqbzeUGA kZcCfIqImxzpbKeCXFdTnb4nKQSFzY4zLXavox9VLjrr4sx76rxhF91hi8B8peLt EcwxSr9ytqOtjkkWSkI3bXIE9CKapzDTWcBa4ezHHoPoZvDznQ7OV9JBU0BGInpS Fa5IYfTdl7cAawxkaTlomTBAwthJ08UQp1DwJRmxcyYm5FN8ktvX7u0YK3RO1zXb ykfpslIlVIZMvRci0xtI5SsOHQWF63PJODLtnwl90759wYhZI8qFfdw/i0qc/HRU +Y0T79lE7eZf10FKhTXFDeweDkUc1xgc5JrCdVUmPcSS9NMR8MGL96Rm938PbJE6 fg/fM00BZ85T3BHDoIHKPRXdUIV0MDkmEw8Z0yeuKDYDPJ+SE+CjVPhHByeiB1hH 3kUeWbHrWgSdp0OYJuhHoUjBfJAlAUDSeYOy9vKi4LN1ZYG3acQl0LAfxYPgOE92 cs4+BqCgZ7vastYET5DqiLodrmNkDGwdnm3O5XVQS2fCZT7RePpmboMpHgDMDaO3 OgavZ9RpJdt5h68GAOE9Q/IK+Y7bblBfRrSrANpvUIWXfLei+IFaQZPTN59v9J8v OwHSq4H74l/MQ8b+q+bhjU472QJZ2m6otO1KkNG4pqOIgtiqYnWrp36uMqWsjYHK aoFRah4xHnutVPa0eh09 =xBnU -END PGP SIGNATURE- ___ 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] HTML form of select parameter
On Jan 27, 2014, at 9:57 AM, John Chilton chil...@msi.umn.edu wrote:
The swap over happens when
the number of items gets sufficiently large and a jQuery-based widget
called select2 replaces all select boxes in Galaxy - unless explicitly
disabled. I understand the desire to disable this. I am not sure
anyone is really very pleased with select2 for multiple select widgets
- it might be worth just disabling it for multiple select form
elements all together globally. I don't know.
The function 'replace_big_select_inputs' in galaxy.base.js is where the logic
for this code is located. You could avoid applying select2 to selects with
multiple using the following CSS selector on line 261 in place of $('select'):
$('select').not('[multiple]')
Best,
J.___
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[galaxy-dev] datatype for executables
Is there a data type in Galaxy that identifies executables uniquely, eg. from the executable bit in the file perms or some other way? Thanks, -- Ketan ___ 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/
