Re: [galaxy-dev] galaxy server file upload problem

@lists.bx.psu.edu] Sent:Wed , November 19, 2014 23:19 PM Subject:Re: [galaxy-dev] galaxy server file upload problem Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy bei

Re: [galaxy-dev] galaxy server file upload problem

Hi Johngui, Can you specify which request is 404'ing -- the exact URL that's being attempted? And, can you provide a little more of your nginx configuration? Is galaxy being served at the root of the domain? -Dannon On Wed, Nov 19, 2014 at 2:01 AM, 홍종희 wrote: > Hi galaxy-dev members > > >

[galaxy-dev] galaxy server file upload problem

Hi galaxy-dev members Recently we're trying to setup the galaxy server in a production mode. Everything seems to be ok but when I tried to upload a file it shows error message like this Failed: Not found(404) I found one thread in galaxy-dev fourn about this one It says that it's because of

Re: [galaxy-dev] Galaxy Data Sources and Dataset Collections

These are all good ideas but I don't think any of the constituent parts are currently possible (symbolic linking outside of libraries, tools that create collections, data sources that create collections, starting workflows with data source tools - there is some bug that prevents GenomeSpace from wo

[galaxy-dev] Galaxy Mailing Lists are moving

Hello Galaxy Community, *Galaxy Mailing Lists are moving!* During the week of November 17-21, 2014, Galaxy mailing lists (including this one) will be migrated from lists.bx.psu.edu to lists.galaxyproject.org . This transition should be largely transparent to you, but there are a few things to be

[galaxy-dev] Galaxy Data Sources and Dataset Collections

Hello, I've been spending a bit of time looking over Data Sources for Galaxy. I've been thinking about designing a tool in Galaxy, similar to a Data Sources tool, which would take as input a file defining a list of URLs to import into Ga

Re: [galaxy-dev] Galaxy Not Displacing History

Hi Dannon, Clearing the browser cache worked! Thanks so much. Jeremy Liu On Thu, Nov 6, 2014 at 2:04 AM, ofer fridman wrote: > I Had the same problem, after moving to stable everything is working. > I know it's not a solution but for the meantime this is what I have. > > Best, Ofer > > On Wed N

Re: [galaxy-dev] Galaxy Not Displacing History

I Had the same problem, after moving to stable everything is working. I know it's not a solution but for the meantime this is what I have. Best, Ofer On Wed Nov 05 2014 at 11:04:01 PM Dannon Baker wrote: > This is usually an old cached version of the history panel interfering, or > a javascript

Re: [galaxy-dev] Galaxy Not Displacing History

This is usually an old cached version of the history panel interfering, or a javascript error that you'd see in the console. Can you clear browser cache, close out all Galaxy windows, and try again? If that still doesn't work, can you look in the javascript console to see if there are any errors?

[galaxy-dev] Galaxy Not Displacing History

Hi Galaxy Dev, I just pulled the latest updates for galaxy-dist with hg pull -u and then migrated over the postgres database with: sh manage_db.sh -c ./universe_wsgi.ini upgrade After restarting the server, my Galaxy instance would not show the history of datasets. The history was still there, s

[galaxy-dev] Galaxy with Rocks Cluster / Submitting Job As Real User

Hi, I've been trying to get Galaxy to submit jobs to my cluster as the "real user" rather than the "galaxy" user. In my galaxy.ini, I have: outputs_to_working_directory = True set_metadata_externally = True drmaa_external_runjob_script = /galaxy/scripts/drmaa_external_runner.py drmaa_external_ki

Re: [galaxy-dev] Galaxy instance file upload problem

As Hans said, this might reguire a change in the proxy server configuration as discussed here: http://gmod.827538.n3.nabble.com/Data-uploaded-with-new-upload-tool-doesn-t-get-added-to-history-td4046375.html On Fri, Oct 17, 2014 at 2:43 AM, Hans-Rudolf Hotz wrote: > Hi Bongsoo > > we had once a s

Re: [galaxy-dev] galaxy-dev Digest, Vol 100, Issue 15

So Ihave finally determined the cause and found a resolution for the snpEff/java problem. The issue was the fact that the vrsion of Java on the Ubuntu linux VM from AWS is 1.6.x snpEff 4.0e requires version 1.7.0 or higher. This is fine, but you willneed to manually upgrade the java version. To

Re: [galaxy-dev] galaxy-dev Digest, Vol 100, Issue 10

So I have finally determined the cause and found a resolution. The issue was the fact that the version of Java on the Ubuntu linux VM from AWS is 1.6.x. GATK2 requires version 1.7.0 or higher. This is fine, but you will need to manually upgrade the java version. To do so you will need to comple

Re: [galaxy-dev] Galaxy instance file upload problem

Hi Bongsoo we had once a similar situation with one of our development Galaxy installations. This was due to a change in the proxy settings of the server. Regards, Hans-Rudolf On 10/17/2014 01:06 AM, Bongsoo Park wrote: Aysam, Thanks for your reply. It works well on usegalaxy.org

Re: [galaxy-dev] Galaxy instance file upload problem

Aysam, Thanks for your reply. It works well on usegalaxy.org, but it doesn't work in the Galaxy instance I've developed. I downloaded the latest Galaxy version, and installed on the Redhat 6.5 system. I created a galaxy user, and just ran it as usual. I have to update any part of the configuration

Re: [galaxy-dev] Galaxy instance file upload problem

Hey Bongsoo, Does this happen on usegalaxy.org? Also does this happen with other files too? Thanks, Sam On Thu, Oct 16, 2014 at 2:49 PM, Bongsoo Park wrote: > Hi folks, > > I encountered the problem in file upload. The error message is like below > 'Failed: Not found (404)'. Attached is the sc

[galaxy-dev] Galaxy instance file upload problem

Hi folks, I encountered the problem in file upload. The error message is like below 'Failed: Not found (404)'. Attached is the screen shot for this error message. Any idea? Thanks! Best, Bongsoo ___ Please keep all replies on the list by usi

[galaxy-dev] Galaxy Training Network

Hello all, We are pleased to announce the *Galaxy Training Network (GTN) *, a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers

[galaxy-dev] Galaxy database corrupted

Recently I tried to upload some annotation/reference files into Galaxy. After couple failed tries using the upload method, I was able to do it via the using the full file path. However, after these tries/retries, I believe Galaxy database got confused and was corrupted. Existing workflows wit

Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library?

Il giorno gio, 02/10/2014 alle 16.50 -0700, Dooley, Damion ha scritto: > I see Galaxy API has a feature to import a history dataset into the > library (in copy_hda_to_ldda() fn from GCC2013 training day course). > Is this available as well via Bioblend? Latest docs don't seem to > include this feat

[galaxy-dev] Galaxy Bioblend option for importing dataset into a library?

I see Galaxy API has a feature to import a history dataset into the library (in copy_hda_to_ldda() fn from GCC2013 training day course). Is this available as well via Bioblend? Latest docs don't seem to include this feature. It would be the opposite of Bioblend's upload_dataset_from_library(h

Re: [galaxy-dev] Galaxy and object stores

Thanks Enis, just to elaborate on Pulsar - I suspect it would work with something like configuring Galaxy with S3 object store right now - but it would do so by having Galaxy cache the data locally and then Pulsar would negotiate the transfer with Galaxy (many different ways this could occur depend

Re: [galaxy-dev] Galaxy and object stores

Hi Inge, There is an implementation for using the AWS S3 object store as the data store for a given Galaxy instance. The implementation is located here https://bitbucket.org/galaxy/galaxy-central/src/3a51eaf209f2502bf32dbb421ecabb7fe46243ea/lib/galaxy/objectstore/s3.py?at=default and it offers seve

[galaxy-dev] Galaxy and object stores

?I have a few questions about object stores in Galaxy: 1: Can all Galaxy data sets be stored in an object store? 2: If so, does Galaxy still need to maintain a local copy of the data? 3: Is LWR or Pulsar able to get the data directly from the object store, or does it still have to go through Ga

Re: [galaxy-dev] Galaxy and HTTPS User-authentification

On Aug 20, 2014, at 3:53 AM, Matthias Enders wrote: > Hi, > > I have a question regarding the user authentication of Galaxy. > > As to my knowledge galaxy uses http, also for the authentication, so the User > Email and the password are send in clear text. > > As I like to use Galaxy for u

[galaxy-dev] Galaxy and HTTPS User-authentification

Hi, I have a question regarding the user authentication of Galaxy. As to my knowledge galaxy uses http, also for the authentication, so the User Email and the password are send in clear text. As I like to use Galaxy for user-authentication and due several disadvantages not an external authenti

Re: [galaxy-dev] Galaxy dont work on my Bio-Linux‏

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can

Re: [galaxy-dev] Galaxy dont work on my Bio-Linux

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can

Re: [galaxy-dev] Galaxy dont work on my Bio-Linux

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can

Re: [galaxy-dev] Galaxy server broken with install of latest changes

Thanks for the update, glad everything is working as expected! On Wed, Aug 13, 2014 at 12:27 PM, Tony Kusalik wrote: > My apologies to everyone. This turns out to be a false alarm. > The problem was caused by a strange, intermittent issue with the > DNS servers on our campus (I'll spare you th

Re: [galaxy-dev] Galaxy server broken with install of latest changes

My apologies to everyone. This turns out to be a false alarm. The problem was caused by a strange, intermittent issue with the DNS servers on our campus (I'll spare you the gory details). The problem boiled down to python on my server not being able to find http://eggs.galaxyproject.org. On Aug 1

Re: [galaxy-dev] Galaxy server broken with install of latest changes

Hey Tony, Thanks for the error report. I'll look into this, but you can try two things really quickly to see if you can get galaxy started: 1) python scripts/fetch_eggs.py may fix up your egg situation 2) just delete the eggs folder of your galaxy distribution (/eggs) and start galaxy again. It

[galaxy-dev] Galaxy server broken with install of latest changes

Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes w

Re: [galaxy-dev] Galaxy error

[jmchil...@gmail.com] > Sent: Tuesday, July 22, 2014 4:06 PM > To: Beck, Emily A > Cc: galaxy-...@bx.psu.edu > Subject: Re: [galaxy-dev] Galaxy error > > Hello, > > Thanks for the bug report. Is this on the main public server (usegalaxy.org) > or a local instance a

Re: [galaxy-dev] Galaxy error

City, IA 52242 > Lab: (319)335-3430 > -- > *From:* John Chilton [jmchil...@gmail.com] > *Sent:* Tuesday, July 22, 2014 4:06 PM > *To:* Beck, Emily A > *Cc:* galaxy-...@bx.psu.edu > *Subject:* Re: [galaxy-dev] Galaxy error > > Hello, > > Thanks for the bug report. Is thi

Re: [galaxy-dev] Galaxy Security Vulnerability

; Date: Thu, 31 Jul 2014 14:55:57 -0400 > From: Nate Coraor > To: Galaxy Development , > galaxy-annou...@lists.bx.psu.edu > Subject: [galaxy-dev] Galaxy Security Vulnerability > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > A security v

Re: [galaxy-dev] Galaxy Security Vulnerability

hand? Regards, Damion Message: 7 Date: Thu, 31 Jul 2014 14:55:57 -0400 From: Nate Coraor To: Galaxy Development , galaxy-annou...@lists.bx.psu.edu Subject: [galaxy-dev] Galaxy Security Vulnerability Message-ID: Content-Type: text/plain; charset="us-ascii" A security v

Re: [galaxy-dev] galaxy install nginx

The order is not very important… however I would install nginx and postgres at the same time, then galaxy. brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist On Aug 1, 2014, at 10:10 AM, ngsf...@hygenomics.com wrote: dear sir:

[galaxy-dev] galaxy install nginx

dear sir: nginx postgress galaxy which one first install ? ngsf...@hygenomics.com ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy l

[galaxy-dev] Galaxy Security Vulnerability

A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python "pickle" functionality to decode state information from tool forms. Because pickles can b

Re: [galaxy-dev] galaxy won't start

, Dori -Original Message- From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Tuesday, July 29, 2014 10:00 AM To: Sajdak, Doris Cc: Galaxy Dev Subject: Re: [galaxy-dev] galaxy won't start Hi Dori, If you haven't updated galaxy or manipulated the eggs at all, then it mi

Re: [galaxy-dev] galaxy won't start

Hi Dori, If you haven’t updated galaxy or manipulated the eggs at all, then it might be an updated system python module interfering with galaxy’s resolution of the pyyaml we ship. Can you try running galaxy from an clean virtualenv? (https://wiki.galaxyproject.org/Admin/Config/Performance/Prod

[galaxy-dev] galaxy won't start

I'm suddenly getting this error today when I tried to restart Galaxy: Starting galaxy... Some eggs are out of date, attempting to fetch... Warning: setuptools (a dependent egg of sqlalchemy-migrate) cannot be fetched Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg One of Ga

Re: [galaxy-dev] [galaxy-iuc] writing datatypes

Before we go too much further down this path with dataytpes, I'm wondering if some of us should put together a spec of some kind that allows us to all agree on the direction. For example, I'm wondering if datatyps should be versioned and have a name-spaced identifier much like the Tool Shed's g

Re: [galaxy-dev] [galaxy-iuc] writing datatypes

Hi Björn, On Jul 22, 2014, at 6:01 PM, Björn Grüning wrote: > Hi Greg, > > thanks for the clarification. Please see my comments below. > >> On Jul 20, 2014, at 3:22 PM, Peter Cock wrote: >> >>> On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning wrote: Hi, single datatype defini

Re: [galaxy-dev] [galaxy-iuc] writing datatypes

Hi Greg, thanks for the clarification. Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock wrote: On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning wrote: Hi, single datatype definitions only work if you haven’t defined any converters. Let's assume I have a datatype X and w

Re: [galaxy-dev] Galaxy error

Hello, Thanks for the bug report. Is this on the main public server (usegalaxy.org) or a local instance at the University of Iowa? -John On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A wrote: > > Hello, > > I have repeatedly gotten the following error message when attempting to > use both the

Re: [galaxy-dev] Galaxy+Toolshed Docker image?

Hi Kyle, not that I know of, but I'm interested in adding such a feature on top of the base galaxy image. You can find the Dockerfile here: https://github.com/bgruening/docker-recipes Ciao, Bjoern Am 21.07.2014 15:39, schrieb Kyle Ellrott: I know there is a base docker image for Galaxy stab

[galaxy-dev] Galaxy+Toolshed Docker image?

I know there is a base docker image for Galaxy stable ( https://registry.hub.docker.com/u/bgruening/galaxy-stable/), but is there a docker image that will start both a server and a toolshed sever and link them? I was hoping that I could use something like that for testing shed based tool deployment

[galaxy-dev] Galaxy error

user usernameemilybeck quota_percent 19 total_disk_usage52086193970 nice_total_disk_usage 48.5 GB email emily-b...@uiowa.edu is_adminfalse tags_used model_class User id 03f0554e2314759e source HDACollection(f313d1d65c4ee57e,451) xhr readyState 4 respo

[galaxy-dev] Galaxy error

Hello, I have repeatedly gotten the following error message when attempting to use both the mapping and pileup functions in Galaxy. I am using files that I have previously used successfully with these functions, and cannot fix it. Thank you. ~Emily Beck user usernameemilybeck quota

[galaxy-dev] Galaxy/ODoSE - Output accessory orthologous genes ERROR

Dear Galaxy team, I am having a problem running Galaxy/ODoSE. In the step "Extract & categorize orthologs", I selected the option "Output accessory orthologous genes" but it didn't work and didn't output any file. The stdout contains multiple warnings: ... WARNING 15:18:06 select_taxa.select_

Re: [galaxy-dev] Galaxy mobile site

Thanks for the link -- easy enough, though a bit crude, if I may say so. If that's the only existing implementation then I think we'll look into making our own improvements, perhaps to share with the community. Assuming we have time, of course...! -- Dr. Mark Rogers Research Assistant Intelligent

Re: [galaxy-dev] Galaxy mobile site

Hi Mark There used to be a nice one: try adding '/mobile" to your galaxy url. It is still kind of working (just without the graphics), and it is sufficient to monitor jobs. Hans-Rudolf There used to be one. On 06/26/2014 08:03 AM, MF Rogers wrote: I hope this isn't a FAQ; I have not yet

[galaxy-dev] Galaxy mobile site

I hope this isn't a FAQ; I have not yet found the question (or answer) online, though I can't imagine I'm the first to ask: Are there plans to make a mobile version of the Galaxy website? Many of the biologists with whom I work would like to be able to monitor and start Galaxy jobs from their iPh

Re: [galaxy-dev] Galaxy Tool Wrapper/DTD/Schema Needed

Your question was answered in the negative on biostar a few days back: https://biostar.usegalaxy.org/p/8101/ Contributions welcomed. On Sat, Jun 21, 2014 at 8:25 AM, Jones, Tyler William < tyler.jo...@coyotes.usd.edu> wrote: > Hi, > > > I am working for USD Bioinformatics and trying to integrat

[galaxy-dev] Galaxy Tool Wrapper/DTD/Schema Needed

Hi, I am working for USD Bioinformatics and trying to integrate Galaxy tools in an application. I have been looking at this site: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax? but was wondering if there was anyway to get the actual DTD or Schema for your tool definitions. Is

Re: [galaxy-dev] galaxy-dev Digest, Vol 96, Issue 14

This is a new one for me. What configuration are you using for both your 'database_connection', and the 'amqp_internal_connection' in your universe_wsgi.ini? On Fri, Jun 13, 2014 at 12:29 AM, xlwang wrote: > Hello, > when i run my galaxy instance type: > $ sh run.sh > I get some error like

Re: [galaxy-dev] galaxy-dev Digest, Vol 96, Issue 14

Hello, when i run my galaxy instance type: $ sh run.sh I get some error like this: Traceback (most recent call last): File "/export/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 38, in app_factory from galaxy.app import UniverseApplication File "/export/galaxy-dist/lib/g

Re: [galaxy-dev] Galaxy updated botched?

...@gmail.com] Sent: Thursday, June 12, 2014 9:16 AM To: Hans-Rudolf Hotz Cc: John Chilton; Kandalaft, Iyad; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy updated botched? Hey Hans (and anyone else using MySQL), Just to clarify -- MySQL doesn't have this (particular) error by default and as lo

Re: [galaxy-dev] Galaxy updated botched?

Hey Hans (and anyone else using MySQL), Just to clarify -- MySQL doesn't have this (particular) error by default and as long as your server default table type has not and does not change you should be fine. I've just successfully tested MySQL using MyISAM all the way to the current tip revision a

Re: [galaxy-dev] Galaxy updated botched?

On 06/12/2014 12:06 AM, John Chilton wrote: If anyone out there has tired using Galaxy with strictly MyISAM tables and found it untenable - by all means please chime in. Well, due to several reasons we are (still) using MySQL (version: 5.1.69) with only MyISAM tables. We have been runnin

Re: [galaxy-dev] Galaxy updated botched?

du Canada > > > > > > From: Dannon Baker [mailto:dannon.ba...@gmail.com] > Sent: Wednesday, June 11, 2014 10:23 AM > To: John Chilton > Cc: Kandalaft, Iyad; galaxy-...@bx.psu.edu > Subject: Re: [galaxy-dev] Galaxy updated botched? > > > > Hey Iyad, > > I j

Re: [galaxy-dev] Galaxy updated botched?

e 11, 2014 10:23 AM To: John Chilton Cc: Kandalaft, Iyad; galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy updated botched? Hey Iyad, I just want to second (and add slightly) to what John said here. I had also failed to reproduce this locally, but that makes perfect sense now -- I'm

Re: [galaxy-dev] Galaxy updated botched?

Hey Iyad, I just want to second (and add slightly) to what John said here. I had also failed to reproduce this locally, but that makes perfect sense now -- I'm glad you figured it out, and thanks for looking into this so closely and reporting back. Like John said, I wouldn't modify the migration

Re: [galaxy-dev] Galaxy updated botched?

Spent a couple hours yesterday trying to track down this - I was not getting anywhere though and I see why now. Well this definitely an unfortunate situation - but I think documentation improvements are the right fix not enforcing the engine type in sqlalchemy migrations. For one, I don't think we

Re: [galaxy-dev] Galaxy updated botched?

This is a follow up for those that are interested with regards to my failed schema upgrade. I believe I have determined why all the tables are set to use the MyISAM engine. When I initialized galaxy on our enterprise servers, they were running a dated version of CentOS. Hence, the OS defaults

Re: [galaxy-dev] Galaxy updated botched?

Hi Everyone, This is follow-up information/questions to the issue I ran into with the galaxy June 2nd, 2014 update. I hope to receive feedback on how to proceed. Background: - Running Galaxy (DB Schema 118) with a MySQL 5.5 back-end - When updating galaxy to the june 2nd rel

[galaxy-dev] Galaxy updated botched?

Hi everyone I was looking to upgrade galaxy to the latest verison. I did the usual hg pull; hg update;. I start up galaxy, it fetches some eggs, and then it tells me that I need a DB schema update. Fine, I ran sh db_manage.sh upgrade. All I see is a list of stack traces similar to the follow

Re: [galaxy-dev] galaxy is not sourcing tool environment

aahh, that must be it, thanks Bjoern! I have the symbolic link, but I did not have the 'requirements' section correct. thanks so much for your help, Isabelle On 6/5/14 9:27 AM, "Björn Grüning" wrote: >Hi Isabelle, > >can you show us the "requirements" section from your tool? >Also you need

Re: [galaxy-dev] galaxy is not sourcing tool environment

Hi Isabelle, can you show us the "requirements" section from your tool? Also you need to have a symbolic link from tool_dependency_dir/hhsuite/2.0.16/ ponting to tool_dependency_dir/hhsuite/default/ In tool_dependency_dir/hhsuite/default/ should be the env.sh file. If you have the correct "r

Re: [galaxy-dev] Galaxy customized tool config file

Thanks Bj ​ örn! for pointing the right issue card, I uplifted those. Vipin On Wed, Jun 4, 2014 at 12:45 PM, Bj ​​ örn Grüning wrote: > Hi Vipin, > > that is currently not possible but a high priority of the Galaxy deavteam. > You can follow the status in several trello cards: > > https://trell

Re: [galaxy-dev] Galaxy customized tool config file

Hi Vipin, that is currently not possible but a high priority of the Galaxy deavteam. You can follow the status in several trello cards: https://trello.com/c/VizlCET9 https://trello.com/c/phMelslw Ciao, Bjoern Am 04.06.2014 18:33, schrieb Vipin TS: Sorry for re-posting! any suggestions to ma

Re: [galaxy-dev] Galaxy customized tool config file

Sorry for re-posting! any suggestions to make an interactive tool page. Thanks you, Vipin On Tue, May 20, 2014 at 5:25 PM, Vipin TS wrote: > Hello dev-team, > > With the current state, is it possible to write an interactive page for a > tool in Galaxy? > > In my case, I m considering to build

Re: [galaxy-dev] Galaxy reports crashing with the latest stable release

Hi Dannon, after removing the *pyc files and killing manually the daemon (--stop-daemon did not work) fixes the problem for me. Sorry for the noise! Bjoern Am 04.06.2014 13:52, schrieb Dannon Baker: I'm having trouble reproducing this. The base grid object that's used by the SpecifiedDateLis

Re: [galaxy-dev] Galaxy reports crashing with the latest stable release

I'm having trouble reproducing this. The base grid object that's used by the SpecifiedDateListGrid does have that info_text field -- it's almost as if you're somehow using an outdated grid module, while the rendering template is current. It's a bit brute force, but can you try (from the base of yo

[galaxy-dev] Galaxy reports crashing with the latest stable release

Hi, I encountered the following bug during my testing of the latest stable release: Error - : 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.

[galaxy-dev] galaxy is not sourcing tool environment

I am using env.sh to manage my tool dependencies: # tool_dependency_dir/hhsuite/2.0.16/env.sh export HHPRED_DIR=/opt/galaxy-dist/tool_dependencies/hhsuite/default export HHLIB=${HHPRED_DIR}/lib/hh export PATH=${HHPRED_DIR}/bin:${HHLIB}/scripts:$PATH Galaxy is not sourcing it. I have to manually

Re: [galaxy-dev] Galaxy queue

galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy queue On 05/26/2014 10:00 AM, Peter Cock wrote: > Hi Neil, > > Via the GUI, if you are logged in as an administrator > (i.e. your email address is listed in universe_wsgi.ini) > there is a an admin tab (top banner, starting analyze >

Re: [galaxy-dev] Galaxy queue

On 05/26/2014 10:00 AM, Peter Cock wrote: Hi Neil, Via the GUI, if you are logged in as an administrator (i.e. your email address is listed in universe_wsgi.ini) there is a an admin tab (top banner, starting analyze data etc). This includes an option to see the current jobs. Via the command l

Re: [galaxy-dev] Galaxy queue

Hi Neil, Via the GUI, if you are logged in as an administrator (i.e. your email address is listed in universe_wsgi.ini) there is a an admin tab (top banner, starting analyze data etc). This includes an option to see the current jobs. Via the command line API? I'm not sure, never looked. Peter O

[galaxy-dev] Galaxy queue

Hi, is there anyway to find out (from the command line or api) what is on the Galaxy queue? When items are queued they appear in grey or processing in yellow can I get hold of these details from the command line as I could then email the user who has just submitted a job with his place on qu

[galaxy-dev] Galaxy is not running

Hi, I am new to Galaxy, so am probably doing something silly. My jobs do not finish and sometimes do not start. Here is the error message: Details user usernamewatterber quota_percent3 total_disk_usage10295907343 nice_total_disk_usage9.6 GB emailatter...@unlv.nevada.edu is_admi

[galaxy-dev] Galaxy customized tool config file

Hello dev-team, With the current state, is it possible to write an interactive page for a tool in Galaxy? In my case, I m considering to build a tool page with JavaScript embed in XML file, my expectation is to behave the Galaxy tool page as google translate page with option instant translation o

Re: [galaxy-dev] galaxy on ubuntu 14.04: hangs on metadata cleanup

It seems to be an NFS related issue. When I run a separate VM as an NFS server that hosts the galaxy data (files, job workdir, tmp, ftp), problems are gone. There’s probably an explanation for that, but I’m going to leave it at this. cheers, — Jorrit Boekel Proteomics systems developer BILS / L

Re: [galaxy-dev] galaxy on ubuntu 14.04: hangs on metadata cleanup

I should probably mention that the data filesystem is NFS, exported by the master from /mnt/galaxy/data and mounted on the worker. No separate fileserver. Master is the one that hangs. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden On 07

[galaxy-dev] galaxy on ubuntu 14.04: hangs on metadata cleanup

Dear all, Has anyone tried running Galaxy on Ubuntu 14.04? I’m trying a test setup on two virtual machines (worker+master) with a SLURM queue. Getting in strange problems when jobs finish, the master hangs, completely unresponsive with CPU at 100% (as reported by virt-manager, not by top). Onl

Re: [galaxy-dev] Galaxy REST API: multiple params per tool

It looks like this is already the case, but only documented in the code (lib/galaxy/webapps/galaxy/api/workflows.py): def _update_step_parameters(step, param_map): """ Update ``step`` parameters based on the user-provided ``param_map`` dict. ``param_map`` should be structured as follo

[galaxy-dev] Galaxy REST API: multiple params per tool

The current method for supplying parameters to tools using the REST API for workflows is fairly broken. The structure is as follow: "parameters":{ "tool_1": { "param":"param_name", "value":"param value" }, "tool_2": { "param":"param_name", "value":"par

Re: [galaxy-dev] Galaxy Error Message

I am running into a problem with coloring of my KEGG image produced. When loading pathview and running this script in R: pv.out<-pathview(gene.data=gse16873.d, pathway.id="04110", species="hsa", out.suffix="gse") you get an image with full coloration. With the same command in galaxy, the image

Re: [galaxy-dev] Galaxy Error Message

Never mind problem solved! Thanks again On Tue, Apr 29, 2014 at 2:40 PM, Bradley Belfiore wrote: > Thank you for your patience and help, I removed the periods and am running > into this error: > > /bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: > Permission denied > > Do

Re: [galaxy-dev] Galaxy Error Message

Thank you for your patience and help, I removed the periods and am running into this error: /bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat: Permission denied Does it have to do with the fact Im using SQLite and not Postgres? On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blanke

Re: [galaxy-dev] Galaxy Error Message

FWIW: looks like a trivial xml syntax error is in this line: interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id $species $out.suffix $output .*..* There seem to be one too many ">" - the first one is pr

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

Hi, I updated the test and the tool shed accordingly to Dave suggestion. I'm just wondering, the TS tests were passing with the old version, anything I should worry about? :) Thanks and sorry for the inconvenience! Bjoern Am 29.04.2014 16:07, schrieb Peter Cock: On Tue, Apr 29, 2014 at 2:59

Re: [galaxy-dev] Galaxy Error Message

Hi Bradley, For your inputs, don’t use periods (‘.’) within the param names. Thanks for using Galaxy, Dan On Apr 29, 2014, at 12:32 PM, Bradley Belfiore wrote: > The XML file is: > > Pathview is a tool set for pathway based data integration > and visualization. It maps and renders a wide

Re: [galaxy-dev] Galaxy Error Message

Upon going back over my script I got it working on the command line as suggested, and when attempting to execute in my instance of galaxy I got this error message which I was not sure about: Traceback (most recent call last): File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py

Re: [galaxy-dev] Galaxy Error Message

The XML file is: Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. interpreter="Rscript"> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data $pathway.id$species $out.suffix

Re: [galaxy-dev] Galaxy Error Message

Hi Brad To me, this looks like an error in tool definition file (ie the xml file). Something like using $gene in the "command" tag without defining it in a "param" tag. But it is difficult to guess without seeing to full xml file. Regards Hans-Rudolf On 04/29/2014 06:13 PM, Bradley Belfior

Re: [galaxy-dev] [galaxy-iuc] Test ToolShed package_samtools_0_1_19 status error?

On Tue, Apr 29, 2014 at 2:59 PM, Dave Bouvier wrote: > Peter, > > Based on the latest test run, and my own investigations, it would appear > that the samtools compilation process is looking in the wrong include path > for ncurses/ncurses_dll.h. My recommendation would be to replace the > following

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