Re: [galaxy-dev] [galaxy-user] List of genomes

Hello Yongde, The list of genomes is gathered from many sources and is comprehensive to facilitate external display functionality (at UCSC - main and microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a standard format to one of these sources, those

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

You can verify this with 'hg branch', but it looks like you're tracking the default branch of -dist, where you want to be on stable. 'hg update stable' should fix this, and the issue you're seeing. You should only have to do this once, next time you update (with just hg pull -u) you'll stay on st

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Dear Dannon, Here is the 'hg tip' result: changeset: 9312:788cd3d06541 tag: tip parent: 9310:19f6e62bd372 parent: 9311:d7f37a2fe690 user:Nate Coraor date:Mon Apr 08 12:30:08 2013 -0400 summary: Merged stable. -- Olivia Le 29/04/13 15:05, Dannon Baker

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Hey, it is not just me! Your commits are definitely in galaxy-dist, they just might not be part of the most recent stable tag. https://bitbucket.org/galaxy/galaxy-dist/commits/80291f7ad4576c95f70eaed2f36cc5a95cf303fb The hg new workflow is easy to mess up, it use to be that you could just trust w

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Olivia, There's a fix for this available in galaxy-central, but I'm surprised you're seeing it in -dist as I thought the problem was introduced after the dist freeze. Can you provide the output of 'hg tip'? -Dannon On Mon, Apr 29, 2013 at 6:53 AM, Olivia Doppelt wrote: > Hello to All, > > I w

Re: [galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Hello to All, I would like to reiterate this problem because it is causing major problems in tha managment of our Galaxy instance Are there some clues on how to solve this issue ? Best regards, -- Olivia Doppelt-Azeroual, PhD Pasteur Institute, Paris Le 23/04/13 22:38, Fabien Mareuil a écr

[galaxy-dev] Galaxy, CloudMan & nginx 1.4.0

I wanted to update CloudMan to use nginx 1.4.0 for web socket proxy support, but I hit a problem. nginx-upload-module does not work with nginx 1.4.0 and the author has no intention of continuing work on the module. https://github.com/vkholodkov/nginx-upload-module/issues/41 There is a patch that

[galaxy-dev] Galaxy API prob with HTTP_REMOTE_USER

Hi all, We encountoured an error with the galaxy api since the last galaxy-dist revision. here is an example of a command line that doesn't work (xxx stand for the admin key) : ./display.py xx http://localhost:18084/api/users we obtain the following error: HTTP Error 50

Re: [galaxy-dev] [galaxy-user] Question about scripting

Hello, I've moved this over to the galaxy-dev list since it concerns a local installation. You'll want to use the 'condor' job running plugin, which is provided with the Galaxy distribution. Have a look at the job_conf.xml.sample_advanced file to see how this would be configured. A very basi

Re: [galaxy-dev] [galaxy-user] Put an apache password on galaxy?

Nevermind, figured it out I needed the directive to be and to use the RewriteCond commands on the Apache/Galaxy webpage. On Tue, Apr 16, 2013 at 5:19 PM, Lee Katz wrote: > Unfortunately my institution at this time requires a password at the > server-level, although I would like to eventually

Re: [galaxy-dev] [galaxy-user] Put an apache password on galaxy?

Unfortunately my institution at this time requires a password at the server-level, although I would like to eventually just use the Galaxy user system (which I am also using anyway) My Apache configuration includes the following in the new virtual host config file, but it isn't working. No passwo

Re: [galaxy-dev] [galaxy-user] Put an apache password on galaxy?

On Apr 16, 2013, at 4:30 PM, Lee Katz wrote: > Thanks Jen. I tried a few more things before posting to galaxy-dev, and it > turns out that I had the default virtual host still running, while I tried to > have a galaxy virtualhost running alongside it. I think it should be > possible to do tha

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Thu, Apr 11, 2013 at 6:03 PM, Nate Coraor wrote: > On Apr 11, 2013, at 12:39 PM, Peter Cock wrote: > >> On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote: >>> Hey Peter, >>> >>> Hopefully Nate will have some wisdom, all I have is a workaround (I >>> have fought with this on multiple forks a

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Apr 11, 2013, at 12:39 PM, Peter Cock wrote: > On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote: >> Hey Peter, >> >> Hopefully Nate will have some wisdom, all I have is a workaround (I >> have fought with this on multiple forks and this is the best I have >> come up with). >> >> Check ou

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Thu, Apr 11, 2013 at 5:02 PM, John Chilton wrote: > Hey Peter, > > Hopefully Nate will have some wisdom, all I have is a workaround (I > have fought with this on multiple forks and this is the best I have > come up with). > > Check out a clean version of the tools branch somehow (it seems lik

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

Hey Peter, Hopefully Nate will have some wisdom, all I have is a workaround (I have fought with this on multiple forks and this is the best I have come up with). Check out a clean version of the tools branch somehow (it seems like the working contents can get stuck in an invalid state that upda

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

(Apologies if this comes twice - it seems I didn't press send when I wrote the draft earlier in the week) On Tue, Feb 19, 2013 at 5:38 PM, Peter Cock wrote: > On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor wrote: >> On Feb 19, 2013, at 12:18 PM, Peter Cock wrote: >> Nate wrote: Hi Peter,

Re: [galaxy-dev] galaxy local installation

On Apr 8, 2013, at 5:01 PM, Yinan Wan wrote: > Hi, > > I was trying to install the galaxy on my laptop and run into the following > error > > Some eggs are out of date, attempting to fetch... > Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > Warning: pycrypto (a dependent egg

[galaxy-dev] galaxy local installation

Hi, I was trying to install the galaxy on my laptop and run into the following error Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent e

Re: [galaxy-dev] Galaxy + ProFTPd - proper configuration / uploaded files not accessible in Galaxy

Hi Björn, yes, this was the problem - I had wrong GID there. Now it works! Thanks! Jan 2013/4/8 Björn Grüning > Hi Jan, > > you have that line in your config file, right? > > SQLNamedQuery LookupGalaxyUser SELECT > "email,password,'1003','1003','/media/data/galaxy_ftp/%U','/bin/bash' > FROM

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

On Mar 21, 2013, at 10:19 AM, wrote: > Hello, > > please could you help me, how to run galaxy directly from my computer? I am > using Bio-Linux (ubuntu distribution) and there is GALAXY already install. > When I try to open it, it is state that: > > "The Galaxy server doesn't seem to be run

Re: [galaxy-dev] Galaxy + ProFTPd - proper configuration / uploaded files not accessible in Galaxy

Hi Jan, you have that line in your config file, right? SQLNamedQuery LookupGalaxyUser SELECT "email,password,'1003','1003','/media/data/galaxy_ftp/%U','/bin/bash' FROM galaxy_user WHERE email='%U'" 1003 is the group ID of your galaxyuser. Try to adjust that number to your ID. Hope that will wo

[galaxy-dev] Galaxy + ProFTPd - proper configuration / uploaded files not accessible in Galaxy

Hi, I am new to Galaxy. I have managed to set up my Galaxy server with PostgreSQL and ProFTPd. I only do not know how to configure the system properly in order to get uploaded files into Galaxy. Problems: 1. I cannot see the files uploaded through ProFTPd from Galaxy. 2. I cannot upload any (even

Re: [galaxy-dev] [galaxy-bugs] Error message when trying to dowload Manhattan plot using the web version

Hi, Regarding the broken download of a composite datatype, as i have commented in https://trello.com/c/25OfmDa1, is due to the temporary folder permissions, where the archived composite datatype is store for download, are set to 0700 and is should be at least 0664, so that the web server can read

Re: [galaxy-dev] Galaxy - FTP Download Problem

Hey Rob, The Cloudman FTP installation (and really, Galaxy's FTP integration in general) is designed only to get files *into* Galaxy, not for downloading. For downloading, you'll want to just use regular HTTP requests. -Dannon On Mon, Mar 25, 2013 at 5:07 PM, Rob Leclerc wrote: > We have a Cl

[galaxy-dev] Galaxy April 1, 2013 Distribution

Galaxy April 1, 2013 Distribution * Complete News Brief * *Highlights:* * Job running configuration changes and refactoring of job runner plugins

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, I've not been able to reproduce the first scenario using a local Galaxy instance against the test tool shed. Could you tell me which revision of Galaxy you're running when you encounter this behavior? I do see that the revision bb20766df19c that you were initially trying to update is

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, I may have been a bit unclear in my previous response. Allow me to illustrate two scenarios: First scenario: 1. A repository is created containing a BWA tool with version 0.5.9 2. The repository is installed to Galaxy. 3. New README file is uploaded, tool version is *not* changed. Se

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, First, allow me to clarify a point of naming: It's not quite right to say "tools" in this situation, as tools are only one of several utilities that a tool shed repository can contain, along with datatypes, workflows, repository dependencies, and so on. This is an important distinctio

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Hey Dave, Thanks against for your quick response! I checked my universe_wsgi.ini file and can confirm that the enabled_tool_shed_check was *commented*. I've uncommented the settings and changed them to: enable_tool_shed_check = True hours_between_check = 1 Then I followed the steps outlined

Re: [galaxy-dev] galaxy not picking up updates from test toolshed

Jorrit, Just to eliminate one possible cause of this behavior, could you confirm that your local Galaxy instance's universe_wsgi.ini file's enable_tool_shed_check setting is uncommented and set to True, and the hours_between_check is also uncommented and set to a value between 1 and 12? -

[galaxy-dev] galaxy not picking up updates from test toolshed

Hey y'all, I noticed that my local galaxy instance doens't pickup latest updates from test toolshed. Steps to reproduce: 1. install obotools from test toolshed using hg clone http://jor...@testtoolshed.g2.bx.psu.edu/repos/jorrit/obotools , revision 45:bb20766df19c 2. hg push new change of ob

[galaxy-dev] Galaxy - FTP Download Problem

We have a CloudMan Galaxy install on Amazon and I'm able to upload FTP files from FireZilla (or programatically through a Java service I wrote). However, I'm unable to download that same file once uploaded. The 550 response is a "Requested action not take. File unavailable (e.g., file not found, n

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

that tool got the following error: URL:http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=5d969cb56112&latest_changeset_revision=f320093f1e8e&

Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username

Thanks John! I'll give it a try. I can't get to that link, it says "forbidden". Do you have another way to access the content? What is the significance of the name 200_runners.py? Thanks! -Greg On Thu, Mar 14, 2013 at 12:43 PM, John Chilton wrote: > Greg, > > I think you can do this with dy

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

Hello, please could you help me, how to run galaxy directly from my computer? I am using Bio-Linux (ubuntu distribution) and there is GALAXY already install. When I try to open it, it is state that:  "The Galaxy server doesn't seem to be running on your machine. You may need to start it w

Re: [galaxy-dev] [galaxy-iuc] Tool Dependency Packages

Repositories that contain only a tool dependency definition file are a special kind of repository. The tool dependency is considered an orphan tool dependency because it is not associated with any tools in the same repository. This orphan designation is not so important in the tool shed itself

[galaxy-dev] galaxy from subdirectory - new history with a page refresh

I have setup a galaxy instance from the root host (without sub-directory) and it's working fine. I have setup another galaxy instance on the same system, but it's being served from a sub-directory using the same front-end Apache. The sub-directory instance creates a new history on every visit o

Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username

Greg, I think you can do this with dynamic job runners. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html Step 1) Set: default_cluster_job_runner = dynamic:///python/default_runner Step 2) Create the file `lib/galaxy/jobs/rules/200_runners.py`, with contents something like thi

Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username

Greg, I don't think there is currently any support for variable substitution of this sort in job runner configuration, but it could definitely be added. Worth filing as an issue. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Mar 13, 2013 at 8:12 AM, greg wrote: >

Re: [galaxy-dev] Galaxy on Cluster - how to set -a flag with username

Hi guys, I just wanted to check in and see if anyone had any ideas on this. (It's actually the -A flag I'm after.) I did try putting this in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8 -A Account_Name/ I was thinking galaxy might substitute the user name for "Account_Name

[galaxy-dev] Galaxy on Cluster - how to set -a flag with username

In our local galaxy install we want the cluster jobs to be run from the galaxy user but we want to include a -a [account name] to our grid software bills properly. Here's what I currently have in universe.wsgi: default_cluster_job_runner = drmaa://-V -pe batch 8/ What I want is something like th

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

shed. I then attempted to "Get Updates" from my local Galaxy instances for that tool got the following error: URL:http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_rev

[galaxy-dev] Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013

Notice Date: Thursday, March 7, 2013 Greetings Galaxy Main & Test Users, The Galaxy Public Main Galaxy Server at http://main.g2.bx.psu.edu (usegalaxy.org) and Test Galaxy Server at http://test.g2.bx.psu.edu will be down on Thursday, March 14, while the t

Re: [galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job

Hi Hans, OK, thanks: diving into the job table. Your question: "why you consider the job as being finished, and Galaxy thinks the job is still running" is the core issue that I need to find out. None of those jobs have entries in the ps list. Currently, I think that those jobs are still list

Re: [galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job

Hi Joachim I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps

[galaxy-dev] Galaxy Reports: 'unfinished jobs' seems not to do the job

Hi all, I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps

Re: [galaxy-dev] [galaxy-iuc] Proteomics category on test toolshed

Hi Greg, I should probably add to this some background info about my dependencies .. which are a bit weird. Basically I have a bunch of repositories that all depend on a rubygem I wrote. This gem is installed under its own gemset using rvm. Installation of this repository is essential befo

Re: [galaxy-dev] [galaxy-iuc] Proteomics category on test toolshed

Thanks Ira, We'll take a look at this as soon as possible and get back to you. Greg Von Kuster On Mar 6, 2013, at 3:45 AM, Ira Cooke wrote: > Hi Greg, > > I should probably add to this some background info about my dependencies .. > which are a bit weird. > > Basically I have a bunch of re

Re: [galaxy-dev] Galaxy: Dependency error htseq_count

date_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=5d969cb56112&latest_changeset_revision=f320093f1e8e&latest_ctx_rev=11 File '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middlewar

Re: [galaxy-dev] [galaxy-iuc] Installing repositories in a specific order

Hi Peter, The problem is that I have multiple repositories in my repository_dependency file ... but they need to be installed in a specific order. I can't seem to get galaxy to install them in the correct order. Ira PS: Sorry about the totally irrelevant subject line ... I've changed it. On

Re: [galaxy-dev] [galaxy-user] Setting up galaxy local server

On Mar 3, 2013, at 5:21 PM, Anusha Nagari wrote: > Hi, > > I am a new user of galaxy and am trying to set up local version of galaxy on > my mac. I followed the instructions in this link and successfully installed > the local version using the following steps: > > mkdir galaxy-python/ > mkdir

Re: [galaxy-dev] [galaxy-iuc] Proteomics category on test toolshed

Hello Ira, Thanks for all of the work you've been doing n your repositories - I've been getting email updates from your repository changes. I'm not quite sure what is causing this behavior. I've taken a glance at your many dependency definitions, and they look correct, so I'm not seeing why c

[galaxy-dev] Galaxy: Dependency error htseq_count

"Get Updates" from my local Galaxy instances for that tool got the following error: URL:http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/&name=htseq_count&owner=lparsons&changeset_revision=5d969cb56112&

Re: [galaxy-dev] [galaxy-iuc] Installing repositories in a specific order

On Tue, Mar 5, 2013 at 10:08 AM, Ira Cooke wrote: > Hi Peter, > > The problem is that I have multiple repositories in my repository_dependency > file ... but they need to be installed in a specific order. I can't seem to > get > galaxy to install them in the correct order. > > Ira > > PS: Sorry

Re: [galaxy-dev] [galaxy-iuc] Proteomics category on test toolshed

On Tue, Mar 5, 2013 at 6:49 AM, Ira Cooke wrote: > Hi, > > I've just uploaded a set of updates to my proteomics tools on the toolshed. > These contain my best attempt to implement automatic dependency installation > ... and for the most part it seems to work. > > I have encountered the following i

Re: [galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data

Hi Rafa, The .loc files in 'tool-data' directory link the index files with the actual paths so you need to configure each of the .loc files to match where the index files are placed. With that, you can put the index files anywhere you'd like on the file system (preferably outside Galaxy's home dire

Re: [galaxy-dev] [galaxy-user] How to create a tool from a script that loads additional source code files?

On Mon, Feb 25, 2013 at 8:02 PM, Samuel Lampa wrote: > Hi, thanks for the quick reply! > > > On 02/25/2013 08:39 PM, Peter Cock wrote: >>> >>> I realize that when the master script ("run.R" in my case) is run, it >>> will >>> >not find the other files, since it is itself moved away to a temporary

Re: [galaxy-dev] [galaxy-user] How to create a tool from a script that loads additional source code files?

Hi, thanks for the quick reply! On 02/25/2013 08:39 PM, Peter Cock wrote: I realize that when the master script ("run.R" in my case) is run, it will >not find the other files, since it is itself moved away to a temporary >working directory (something like >".../galaxy/database/job_working_direct

Re: [galaxy-dev] [galaxy-user] How to create a tool from a script that loads additional source code files?

On Mon, Feb 25, 2013 at 7:11 PM, Samuel Lampa wrote: > Hi, > > I have aGalaxy toolwith some R code which is split up into a few files, > which are loaded by a "master R script", which orcestrates and executes the > whole thing. > > I realize that when the master script ("run.R" in my case) is run,

Re: [galaxy-dev] galaxy-dev mailing list

Hi Oya, This is the link: http://wiki.galaxyproject.org/MailingLists Thanks for using Galaxy, Dan On Feb 20, 2013, at 8:39 AM, Dannon Baker wrote: > Hi Oya, > > Here's a wiki page detailing how to subscribe and unsubscribe from any > of the galaxy mailing lists: > > -Dannon > > 2013/2/14

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux update

[galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data

Hi, I've installed Galaxy in local and following the Tool dependencies manual I installed all necessary tools. However for some of then such as BWA, Bowtie,... it's usually needed to create indexes. Where should I store those indexes?

Re: [galaxy-dev] galaxy-dev mailing list

Hi Oya, Here's a wiki page detailing how to subscribe and unsubscribe from any of the galaxy mailing lists: -Dannon 2013/2/14 Oya Uyguner : > I would like to enroll, galaxy-dev mailing list. > Regards, > Z. Oya Uyguner > Department of Medical Genetics > Istanbul Medical Faculty > Istanbul Univer

[galaxy-dev] Galaxy @ GMOD2013 & Biocuration 2013

Hello all, There are a couple of things going on with the GMOD Project that the Galaxy Community might be interested in. If you aren't familiar with GMOD, it is a federation of open-source projects and tools that enable visualizing, annotating, managing, and analyzing biolog

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor wrote: > On Feb 19, 2013, at 12:18 PM, Peter Cock wrote: > Nate wrote: >>> Hi Peter, >>> >>> This is due to the annoying way in which Mercurial handles symlinks. We're >>> going to graft the changesets that caused this up to stable shortly, but in >>>

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Feb 19, 2013, at 12:18 PM, Peter Cock wrote: > On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor wrote: >> On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: >> >>> Hi all, >>> >>> I've got an hg puzzle, can anyone on the Galaxy team explain the >>> cause of this and what action I can take to avoid

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor wrote: > On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: > >> Hi all, >> >> I've got an hg puzzle, can anyone on the Galaxy team explain the >> cause of this and what action I can take to avoid it? >> >> Starting with a clean checkout, >> >> $ hg clone

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: > Hi all, > > I've got an hg puzzle, can anyone on the Galaxy team explain the > cause of this and what action I can take to avoid it? > > Starting with a clean checkout, > > $ hg clone https://bitbucket.org/galaxy/galaxy-central > warning: bitbuc

[galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

Hi all, I've got an hg puzzle, can anyone on the Galaxy team explain the cause of this and what action I can take to avoid it? Starting with a clean checkout, $ hg clone https://bitbucket.org/galaxy/galaxy-central warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:

Re: [galaxy-dev] [galaxy-user] Uploading large archive histories

> After discussing this with Getiria, I think what is needed here is a way to > use FTP to upload compressed histories from the import screen as is available > from the upload data tool. The problem we're currently experiencing is that > when we try to upload a compressed history where the com

Re: [galaxy-dev] Galaxy - Bismark

Hi Charles, I will try to fix that as soon as possible. Will get back to you. Bjoern > Hi, > > > I' am running galaxy locally and I have installed Bismark and its > dependencies from the Galaxy main tool shed. I receive multiple errors > when using a small test dataset. > > > (1) My first er

[galaxy-dev] Galaxy - Bismark

Hi, I' am running galaxy locally and I have installed Bismark and its dependencies from the Galaxy main tool shed. I receive multiple errors when using a small test dataset. (1) My first error occurs when I try running Bismark bisulfite mapper (bowtie2): Error indexing reference sequence /bin/s

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

It's really hard to say what's going on with those issues without more information about the particular version of galaxy (which unfortunately we'd get from `hg tip`, which won't work on your bio linux install) or proxy configuration, if any. I'm also not sure what the appropriate bio linux update

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

I still haven't heard back from the Bio-Linux guys regarding how to update Galaxy within Bio-Linux... In the meantime, I tried to play with the "Manage data libraries", in order to import large datasets. I modified the "library_import_dir" line in the universe_wsgi.ini. The first thing I can say i

[galaxy-dev] galaxy-dev mailing list

I would like to enroll, galaxy-dev mailing list. Regards, Z. Oya Uyguner Department of Medical Genetics Istanbul Medical Faculty Istanbul University Bu elektronik posta ve beraberinde iletilen bütün dosyalar sadece göndericisi tarafindan alinmasi amaçlanan yetkili gerçek ya da tüzel kisinin kullan

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

This could be the problem, I just installed BioLinux 7 on my computer with Galaxy running out-of-the-box... However, it looks like they changed a few things, there is no .hg file and no galaxy-dist folder. Can I update outside of mercurial? 2013/2/13 Dannon Baker > How old is the galaxy you're

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

Ok, one more step closer (I thought closing the browser would be enough to restart galaxy, but obviously, I had to reboot the computer). But now it says: ValueError: too many values to unpack 2013/2/13 Dannon Baker > On Feb 13, 2013, at 6:16 PM, David Joly wrote: > > > Hi! > > > > Ok, I know

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

How old is the galaxy you're running? To use the main toolshed you'll need to use a galaxy-dist release from December or later. After this point in time the interface was standardized and is backwards compatible. To update, you should be able to simply navigate to your galaxy-dist directory,

Re: [galaxy-dev] [galaxy-user] Installing new tools from the tool shed

On Feb 13, 2013, at 6:16 PM, David Joly wrote: > Hi! > > Ok, I know many people had the same issue, but I just can't figure what's > going on. I'm quite new about using a local instance of Galaxy and I'm trying > to figure how to install a tool from the tool shed. Reading the tutorial > (Ins

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

Thanks Dannon. BR Zeeshan On W7-Feb 12, 2013, at 12:22 PM, Dannon Baker wrote: > Yes, you use the same image for both masters and the workers. > > -Dannon > > On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah wrote: > >> Thanks Enis, >> The paper is good , i was looking something like it. >

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

Yes, you use the same image for both masters and the workers. -Dannon On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah wrote: > Thanks Enis, > The paper is good , i was looking something like it. > > Ok, I will use CBL , just a small query : > > we use CBL for cloud man purpose, i think yes .

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

Thanks Enis, The paper is good , i was looking something like it. Ok, I will use CBL , just a small query : we use CBL for cloud man purpose, i think yes . Should we use the same Image for workers and enable cloudman script to use that one for launching nodes ? BR Zeeshan On W7-Feb 11, 2

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

Here's a link to the architecture paper: http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full Building CloudMan image from the repo you mention will not work - that repo is for cloudman itself while you need an image capable of running cloudman. For that, you should use CBL. Also, here are so

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

Hi, Thanks for answers , Actually i tried to understand cloudman role in galaxy , do you have an architecture paper which i should read ? for e.g. what i unserstood si that cloud man runs a python server and manage SGE through it via some python script . (may be i am wrong) Our proposed in

[galaxy-dev] Galaxy February 8, 2013 Distribution & News Brief

Galaxy Feb 8, 2013 Distribution & News Brief *Complete News Brief * *Highlights:* * /Improvements/ to our release process

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

As far as actually building the image, the recommended method is to use CloudBioLinux build scripts: https://github.com/chapmanb/cloudbiolinux There is a CloudMan flavor of CBL that allows you to build only CloudMan- and Galaxy-required parts: https://github.com/chapmanb/cloudbiolinux/tree/master/c

Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?

The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Cloudman handles managing NFS for you and sharing the gala

Re: [galaxy-dev] galaxy error

Hi Bassam, I think that your best bet is to explore this command usage in general, since this is really a unix question and no detail about how you used this in Galaxy was provided for others to comment on. I am assuming that you already checked your Galaxy process and found out if it already

[galaxy-dev] galaxy error

Hi Bassam, First, I am going to post your question to the galaxy-...@bx.psu.edu mailing list. This is where local and cloud install Galaxy questions can get the best exposure to the development community. Next, this isn't necessarily an error. And was the full line really this? nohup: ignori

Re: [galaxy-dev] galaxy api documentation

-Original Message- > > From: Dannon Baker [mailto:dannonba...@me.com] > > Sent: Saturday, February 02, 2013 10:57 PM > > To: Rose Mark USRE > > Cc: galaxy-dev@lists.bx.psu.edu > > Subject: Re: [galaxy-dev] galaxy api documentation > > > > Mark, &g

Re: [galaxy-dev] galaxy assumed linux shell

Command lines inside tool configs are assumed to be 'sh' (posix bourne shell). If you are extending one of the runners, definitely stick to pure 'sh'. However, once your command is run, there is no reason you can't use any shell of your choice. -- James Taylor, Assistant Professor, Biology/CS, E

[galaxy-dev] galaxy assumed linux shell

Hi, There are couple of Linux shells: bash, sh, zsh, csh. etc I would like to know if Galaxy is written to be supported on a specific one or it is written to support any linux shell? I'm asking this, because I want to add some features and I want to know what shell should I support? Or should writ

Re: [galaxy-dev] galaxy api documentation

gt; Thanks again for your help > > Mark > > -Original Message- > From: Dannon Baker [mailto:dannonba...@me.com] > Sent: Saturday, February 02, 2013 10:57 PM > To: Rose Mark USRE > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] galaxy api d

Re: [galaxy-dev] galaxy api documentation

: Saturday, February 02, 2013 7:57 PM > To: mark.r...@syngenta.com > Cc: galaxy-dev@lists.bx.psu.edu > Subject: Re: [galaxy-dev] galaxy api documentation > > Mark, > > There's documentation currently available here: > https://galaxy-dist.readthedocs.org/en/latest/

Re: [galaxy-dev] galaxy api documentation

USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] galaxy api documentation Mark, There's documentation currently available here: https://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html Is there anything else in particular you're looking for? -Dannon

Re: [galaxy-dev] galaxy api documentation

@lists.bx.psu.edu Subject: Re: [galaxy-dev] galaxy api documentation Mark, There's documentation currently available here: https://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api. html Is there anything else in particular you're looking for? -Dannon On Feb 2, 2013, at 9:15

Re: [galaxy-dev] galaxy api documentation

Mark, There's documentation currently available here: https://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html Is there anything else in particular you're looking for? -Dannon On Feb 2, 2013, at 9:15 PM, mark.r...@syngenta.com wrote: > Hi All > > When is it anticipa

[galaxy-dev] galaxy api documentation

Hi All When is it anticipated that the documentation for the API will be available? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by

Re: [galaxy-dev] Galaxy with EMBOSS 5 or EMBOSS 6 ?

> You're right -- the EMBOSS version supported by the Galaxy wrappers is > currently EMBOSS 5. We do have a Tool Dependency page here: > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but > unfortunately while it lists versions for many tools it doesn't cover them > all. I'll upda

<    1   2   3   4   5   6   7   8   9   10   >