Re: [galaxy-dev] multiple input files

Sorry, my answer doesn't fit your question. :-) J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote: Hi Ulf, What I do: 1. make a history, doing the steps you want to do on one input file 2. create a workfl

Re: [galaxy-dev] multiple input files

Hi Ulf, What I do: 1. make a history, doing the steps you want to do on one input file 2. create a workflow of that history 3. assemble all input files in one history 4. run the workflow and select the multiple input files to run the workflow on. 5. Optionally: send the results to a new history,

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

next step in the dependencies file gives an error: mv: cannot stat transpose.zip': No such file or directory Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:06 PM, Peter Cock wrote: You must escape any ampersand in the XML as &am

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

#x27;t believe they need to be escaped, since they're not XML entities like the ampersand is. The following download_by_url action should work: http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip --Dave B. On 09/30/2013 08:45 AM, Joachim J

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

load_by_url">http://downloads.sourceforge.net/project/transpose/transpose/transpose-2.0/2.0/transpose-2.0.zip --Dave B. On 09/30/2013 08:45 AM, Joachim Jacob | VIB | wrote: Hi all, Not fixed yet. Somehow the download does not work: I have escaped the ampersands and the hyphens. T

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

AM, Joachim Jacob | VIB | wrote: Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and installed it. After applying some changes to the tool, I 'hg push'ed the changes to my

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

See attachment. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:15 PM, Peter Cock wrote: On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | wrote: Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I

Re: [galaxy-dev] Download URL not accepted in tool_dependencies.xml

such file or directory Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:06 PM, Peter Cock wrote: You must escape any ampersand in the XML as & and then it should work. Peter On Mon, Sep 30, 2013 at 12:51 PM, Joachim Jacob | VIB

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and installed it. After applying some changes to the tool, I 'hg push'ed the changes to my repository on my toolshed. I uninstalled the t

[galaxy-dev] Download URL not accepted in tool_dependencies.xml

Hi all, The download URL seems not to be accepted in tool_dependencies.xml. It is an URL from sourceforge, the direct link to a package. The error upon uploading the tool to my toolshed: ** Metadata may have been defined for some items in revision '5665a799775d'. Correct the foll

Re: [galaxy-dev] ZFS storage recommendations

cause a significant write penalty. If you can suffer the decreased space optimization, lzjb performs significantly better than gzip. gzip-1 is a nice compromise between the default gzip level and lzjb, as well. --nate On Sep 11, 2013, at 3:45 AM, Joachim Jacob | VIB | wrote: Thank you all for the

Re: [galaxy-dev] Stable Galaxy for local install

The latest code from the 'stable' branch of Galaxy is preferred. See the news brief accompanying the update (release_2013.08.12) on http://wiki.galaxyproject.org/DevNewsBriefs/2013_08_12 You need mercurial (http://mercurial.selenic.com/) for installing Galaxy. Report bugs at https://trello.com/

Re: [galaxy-dev] Deseq2 wrapper question

isibility? You could even have the Tool Shed itself require a search step before creating a new repository to avoid accidental duplication of effort? Or maybe a wiki page of wrappers in progress? (And maybe we should split this into a new thread) Regards, Peter On Wed, Sep 11, 2013 at 8:59 AM, Joac

Re: [galaxy-dev] Deseq2 wrapper question

Hi Rui, I should provide a 'sample metadata table', a tabular file with one column the names of your samples, the other column the associated metadata (e.g. type). This is how I've done it in my DESeq2 wrapper. :-) Feel free to check the interface at http://toolshed.bits.vib.be/view/joachim/

Re: [galaxy-dev] ZFS storage recommendations

t ZFS configuration, much more than you will glean from few posts here. http://zfsonlinux.org/lists.html cheers, Simon -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev- boun...@lists.bx.psu.edu] On Behalf Of Joachim Jacob | VIB | Sent: Tuesday, 10 Septemb

[galaxy-dev] ZFS storage recommendations

Hi all, I am performing some tests to move my galaxy database to ZFS. Does anybody have experience with ZFS on linux, and some recommendations/experiences to optimize performance? The purpose is to share the database over NFS to the Galaxy VM. Thanks, Joachim. -- Joachim Jacob Contact deta

Re: [galaxy-dev] API question: is it possible to start exporting histories

OK, I would like to see that happen too :-) I have been thinking about possible 'elegant' solutions to enable this exporting. I am very enthousiastic about Bittorrent Sync, which could perhaps be an efficient and secure way to export the histories (http://labs.bittorrent.com/experiments/sync.h

[galaxy-dev] API question: is it possible to start exporting histories

Hi all, Is it currently possible to export histories via the API? I have one user who want to download and store her data. Total sizes of all her histories combined is about ~700GB. I think this is a typical API job: to list all her histories, start 'exporting to file' all of them, and final

Re: [galaxy-dev] Solved Tool's toolshed page does not get updated after uploading new version

Hmm, now the tool's page is updated. Problem solved. Perhaps a browser cache issue or something alike. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/06/2013 10:22 AM, Joachim Jacob | VIB | wrote: Hi all, My issue: I have put a new version of a to

[galaxy-dev] Tool's toolshed page does not get updated after uploading new version

Hi all, My issue: I have put a new version of a tool in our local toolshed (via 'hg push'). Now, going to the tool's page, still the old version of the README is displayed. When browsing the repository, the new (last uploaded) version is there. In addition, the tool's page show the latest rev

Re: [galaxy-dev] ProFTPD Config Issues

Hi Adam, I remembered having a hard time getting this to work. After it worked, networkadmins decided to disallow ftp connections at our university due to security concerns... I do not remember the solution (...), but I can share my config files (I am using apache instead of nginx): This

Re: [galaxy-dev] Trackster: alignment is not showing up as 'squish'

Update: the 'dense' option does not work neither. So in summary: the alignment can only be viewed in 'coverage' mode. Thanks, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/05/2013 09:52 AM, Joachim Jacob | VIB | wrote: Hi all

[galaxy-dev] Trackster: alignment is not showing up as 'squish'

Hi all, I have a problem that the mappings of an experiment suddenly don't show up anymore in Trackster, only when I choose 'squish' as visualisation format. 'Coverage' and 'dense' provide the expected output. So 'squish' shows nothing. But 'Pack' shows only the names, without the bars. Note:

Re: [galaxy-dev] Galaxy Release Cycle Length

I follow Peter. Shorter release cycles, and I will likely skip updates (as I have done in the past). Longer, and I am starting to implement patches on bitbucket myself to bugs I found, instead of waiting for the next release (which sometimes annoys mercurial - when appropriate I ask for a pull

Re: [galaxy-dev] UGENE tools integration into Galaxy web-platform

Hi Peter, I have used UGene before: it is a nice tool. I am not sure I have understood your question. The easiest way to integrate your tool in Galaxy, is that your tool can be driven by the command line (no GUI). The tool and parameters should be configured by a tool config file, as you men

Re: [galaxy-dev] Disable cheetah filtering

Hmm, seems that collaborating on tools is kind of a burden... Three places to notify this small change you say? (trello, galaxy-dev and direct emailing to the authors.) I have opted for Trello, card #1013 Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

Re: [galaxy-dev] Disable cheetah filtering

tool? Can somebody of the devteam grant me acces? Do I send the diff by email :-) ? Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:17 AM, Peter Cock wrote: On Wed, Jul 24, 2013 at 9:40 AM, Joachim Jacob | VIB | wrote: Hi all,

Re: [galaxy-dev] Disable cheetah filtering

Thanks both of you! Okay, so I was looking in the wrong direction. This solved the issue. Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 07/24/2013 11:13 AM, Björn Grüning wrote: Hi Joachim, try that one: http://wiki.galaxyproject.org/Admin

[galaxy-dev] Disable cheetah filtering

Hi all, A Cheetah question: when I enter ";" as a value in a text box of a tool (stored in $exp), Cheetah prints this as "X", and passed this string to the tool. How to disable this behaviour in Cheetah? I have tried to play with #filter directives, but to no avail. Thanks, Joachim -- J

Re: [galaxy-dev] Cann't restart server after updating to the latest version

Hi, Please keep questions on the galaxy-dev list. Can you paste the part of your universe_wsgi.ini that is under # --- HTTP server ? Can you also provide the output (as user galaxy) of $ lsof -Pni | grep galaxy I think this error can happen if you try to start Galaxy w

Re: [galaxy-dev] repeat tag enhancement?

I like your proposal. I don't think it is currently possible to add - say - 5 repeat blocks at once. Feel free to add and describe your suggested enhancement on Trello, so I can vote for it :-) http://galaxyproject.org/trello Cheers, Joachim Joachim Jacob Contact details: http://www.bits.vib

Re: [galaxy-dev] Testing with parameters

ontact details: http://www.bits.vib.be/index.php/about/80-team On 07/16/2013 01:49 PM, Joachim Jacob | VIB | wrote: Oops, I was replying via theGalaxy Development List Archive <http://dev.list.galaxyproject.org/> interface, strange it has put the reply off list... So no functional test for my too

Re: [galaxy-dev] Testing with parameters

Oops, I was replying via theGalaxy Development List Archive interface, strange it has put the reply off list... So no functional test for my tool ( despite my enthousiasm :-) ), since the repeat tags must be provided in the test. Thanks, Joachim. Joachim

[galaxy-dev] Possible bug in managing tool shed repositories

Hi all, Before posting on Trello, perhaps someone can confirm that it is a bug: 1. In the admin menu, go to 'Manage installed tool shed repositories' 2. click on a tool that you have installed with dependencies (!) 3. In the top right 'repository actions', choose 'Manage tool dependencies' 4. In

Re: [galaxy-dev] Messed up a tool installation from a local toolshed

ng? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von

[galaxy-dev] Messed up a tool installation from a local toolshed

Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to

Re: [galaxy-dev] Trackster error: not able to find the chrom len file

M, Joachim Jacob | VIB | wrote: Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.

[galaxy-dev] Trackster error: not able to find the chrom len file

Dear all, I updated to the latest Galaxy stable code, and updated the datatypes_conf.xml. Trackster displays an error after opening a saved view: *** Error: The requested genome file (/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/dm3.len) could not be opened. Exi

Re: [galaxy-dev] Installing Galaxy EC2

Hi Daniel, Make also sure you use correct firewall settings ('security groups') in EC2. They are described the Galaxy wiki (http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29), but there are some small differences with the setting applied by CloudLa

Re: [galaxy-dev] Cann't restart server after updating to the latest version

Hi Karen, Can you first switch to the user under which Galaxy runs, and go to the home directory of Galaxy: over there, run ./run.sh and watch which error messages appear. This should give you more information. It is recommended after a update to run Galaxy first like this. Kind regards, Joa

[galaxy-dev] Status of Galaxy Cloud Instance dev

Hi all, I am planning to launch a Galaxy Cloud Instance, to run for about one month. But I believe I've read somewhere a new image of Galaxy on AWS is being prepared right now. Can somebody update me on the status? Perhaps it is smart to wait a few days with launching through CloudLaunch un

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

hu 30 May 2013 11:52:54 AM CEST, Peter Cock wrote: On Thu, May 30, 2013 at 10:30 AM, Joachim Jacob | VIB | wrote: Unfortunately, updating to the latest code (9320:47ddf167c9f1) does not solve the problem. In Trello, this card #584 was posted, mentioning installing compiled binaries is not yet pos

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

ay be due to an issue that was fixed between 9320:47ddf167c9f1 and the current stable branch. I would recommend updating to the most recent stable branch of galaxy-central. --Dave B. On 5/29/13 09:30:37.000, Joachim Jacob | VIB | wrote: Strange. When I just wget that link in a termina

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

as an archive os some kind? Greg Von Kuster On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote: Hi all, I am building a wrapper around BLAT, and have put it locally in a toolshed. However, the automatic installation of dependencies fails: * Tool dependency

Re: [galaxy-dev] Creating tool shed repository: installation of dependencies fails.

determines it as a text file, while Safari displays it. This is the cause of the problem. Is there a different URL to download blat that actually downloads it as an archive os some kind? Greg Von Kuster On May 29, 2013, at 6:54 AM, Joachim Jacob | VIB | wrote: Hi all, I am building a

[galaxy-dev] Creating tool shed repository: installation of dependencies fails.

Hi all, I am building a wrapper around BLAT, and have put it locally in a toolshed. However, the automatic installation of dependencies fails: * Tool dependency installation error: [Errno 2] No such file or directory: '/home/galaxy/galaxy-dist/database/tmp/tmp2J7K_L/da

Re: [galaxy-dev] Workflow: multiple input errors

It is most likely due to the cluster configuration, since on our non-cluster production machine doesn't have this behaviour. Cheers, J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 05/17/2013 10:16 AM, Joachim Jacob | VIB | wrote: Hi all, I have fir

[galaxy-dev] Workflow: multiple input errors

Hi all, I have fired up an cloud instance of Galaxy, 2 persistent nodes, scalable up to 10. I have updated the code to the latest stable, after issues with not being able to select multiple input for workflows (more background: http://dev.list.galaxyproject.org/selecting-multiple-inputs-for-w

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

x27;ll get the extra changesets but they won't be activated when you update) On Thu, May 16, 2013 at 11:08 AM, Joachim Jacob | VIB | mailto:joachim.ja...@vib.be>> wrote: OK. So I believe I can wait for the next stable release then. I assume a do not want to go the default b

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

05:01 PM, Dannon Baker wrote: Your instance isn't quite up-to-date enough for the fix -- it's around 9549:47ddf167c9f1 -central / 9452:94caae7433a7 grafted in -stable. On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB | mailto:joachim.ja...@vib.be>> wrote: Running

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

). On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB | mailto:joachim.ja...@vib.be>> wrote: Hi all, I just found out that I cannot select multiple inputs in workflows anymore in our local Galaxy. This option used to work on these workflows in the past. I only get now a dr

[galaxy-dev] selecting multiple inputs for workflows not possible anymore

Hi all, I just found out that I cannot select multiple inputs in workflows anymore in our local Galaxy. This option used to work on these workflows in the past. I only get now a dropdown box, without the little icon at the top of the input list to select multiple inputs. I am a little puzzl

[galaxy-dev] Cloudman - missing security rules in wiki page

Hi all, I have tried to fire up an Cloud instance of Galaxy following the wiki page: http://wiki.galaxyproject.org/CloudMan However, two attempts failed (Cloudman interface did not come up - I could SSH into the machine). Next, I have tried the CloudLaunch interface (added the link to the wiki

[galaxy-dev] selecting multiple inputs for workflows not possible

Hi all, I just found out that I cannot select multiple inputs in workflows. This option used to work on these workflows in the past. I am a little puzzled of what's wrong. Any light in the dark? Note: I have started a cloud galaxy instance and imported that workflow, but no option to select

Re: [galaxy-dev] starting run_reports.sh fails

@bitsatvib On 05/15/2013 07:00 PM, Dannon Baker wrote: Heh, thanks for answering both halves of the email before I could even get to it :) On Wed, May 15, 2013 at 12:03 PM, Joachim Jacob | VIB | mailto:joachim.ja...@vib.be>> wrote: Already reported in Trello https://trello.com/c/o0

Re: [galaxy-dev] starting run_reports.sh fails

Already reported in Trello https://trello.com/c/o0S3klAF Thanks for the fix! Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote

[galaxy-dev] starting run_reports.sh fails

run_reports.sh dies silently. Its last will in reports_webapp.log states: Traceback (most recent call last): File "./scripts/paster.py", line 33, in serve.run() File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, op

Re: [galaxy-dev] Protocol for changing the section of an installed tool shed repo

Deleting the integrated tool panel config and retarting solved the issue. Thanks! Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 05/08/2013 04:02 PM, Björn Grüning wrote: Hi Joa

[galaxy-dev] Protocol for changing the section of an installed tool shed repo

Hi all, Stupidly enough, I installed a tool shed repo under 'root' of the toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!). 1. From the admin menu, I choose to unactivate the repo (manage tool shed repo's) 2. From the admin menu, I reinstalled the tool shed from Main Tool Sh

Re: [galaxy-dev] Exporting histories fails: no space left on device

xy$1 [P] == Thanks, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/28/2013 03:21 PM, Joachim Jacob | VIB | wrote: OK, it seems to be a proxy error. When the proxy does not re

Re: [galaxy-dev] Exporting histories fails: no space left on device

estraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/28/2013 02:58 PM, Joachim Jacob | VIB | wrote: Hi Assaf, After all, the problem appears not to be total size of the history, but the size of the individual datas

Re: [galaxy-dev] Exporting histories fails: no space left on device

Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On Tue 26 Mar 2013 03:45:43 PM CET, Assaf Gordon wrote: Hello Joachim, Joachim Jacob | VIB | wrote, On 03/26/2013 10:01 AM: abrt was filling th

Re: [galaxy-dev] FTP upload - symlink to uploaded data

Hi Rob, Indeed, I had/have some difficulties with setting temporary directories. The problem was that FTP uploaded data was first copied to TMPDIR prior to being put in the database directory. My solution: I extended the /tmp partition to several GB's, by mounting a bigger device over it.

Re: [galaxy-dev] Exporting histories fails: no space left on device

m Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/25/2013 05:18 PM, Assaf Gordon wrote: Hello Joachim, Couple of things to check: On Mar 25, 2013, at 10:01 AM, Joachim Jacob | VIB | w

Re: [galaxy-dev] Issue with viz of mapped data in Trackster

OK (I see now I have posted twice the same error from the log - silly of me, sorry). First this: yes, the permissions in the data library are set so that only I and one other person can access the data library (set by one sharing role for both of us) The entries in the job table related to t

[galaxy-dev] Exporting histories fails: no space left on device

Hi all, Exporting histories fails on our server: " Reason: *Error reading from remote server". *When looking at the logs and the system: tail /var/log/messages Mar 19 15:52:47 galaxy abrt[25605]: Write error: No space left on device Mar 19 15:52:49 galaxy abrt[25605]: Error writing '/var/spo

Re: [galaxy-dev] Issue with viz of mapped data in Trackster

see if they have any standard out/err that could provide insight into the problem? Thanks, J. On Mar 15, 2013, at 9:47 AM, Joachim Jacob | VIB | wrote: Hi all, Since the last updata of Galaxy, I was not able anymore to view newly added tracks to existing or newly created visualisations. In

[galaxy-dev] Issue with viz of mapped data in Trackster

Hi all, Since the last updata of Galaxy, I was not able anymore to view newly added tracks to existing or newly created visualisations. In the webhandler, I have traced down this error: 193.191.128.2 - - [14/Mar/2013:11:02:13 +0200] "GET /api/datasets/407a09c0b5976b4e?hda_ldda=hda&data_type

[galaxy-dev] Bam to sam error

Hello, I got an error on our local Galaxy using bam-to-sam. The BAM file is a result of a Tophat version 1 run. The error Error sorting alignments from (/mnt/galaxydb/files/006/dataset_6733.dat), error An error occurred with this dataset:/Samtools Version: 0.1.18 (r982:295) Error sorting al

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

[galaxy-dev] Installing htseq-count via Toolshed: error installing dependency.

Hi all, Installing htseq-count with dependencies fails on my system: htseq-count installs four dependencies (numpy, picard, samtools, htseq) , of which one fails (htseq), strangely enough. The error is: error: can't create or remove files in install directory The following error occurred w

[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

[galaxy-dev] Galaxy: Dependency error htseq_count

Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install d

Re: [galaxy-dev] Environment variables reset after manually restarting Galaxy

Coraor wrote: On Feb 11, 2013, at 7:48 AM, Joachim Jacob |VIB| wrote: Hello all, After a *reboot* of our Galaxy server, the environment variables are set correctly. However, after *restarting* the Galaxy process on a running server, by logging in as Galaxy and running the init script on CentOS as

Re: [galaxy-dev] Preffered way of running a tool on multiple input files

nputs and merge them to one. On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| mailto:joachim.ja...@vib.be>> wrote: Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would procee

Re: [galaxy-dev] Preffered way of running a tool on multiple input files

Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would proceed by creating a data library for all your fastq files, which you can upload via FTP, or via a system directory. You can use a sample of your

[galaxy-dev] Bug in Galaxy Reports tool

Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' -> picking a user -> picking a month -> and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat

[galaxy-dev] Environment variables reset after manually restarting Galaxy

Hello all, After a *reboot* of our Galaxy server, the environment variables are set correctly. However, after *restarting* the Galaxy process on a running server, by logging in as Galaxy and running the init script on CentOS as "service galaxyd restart", the environment variables seems to b

[galaxy-dev] Bug Re: Data library not properly showing up

braries" https://trello.com/card/show-roles-associated-with-data-libraries/506338ce32ae458f6d15e4b3/229 cheers Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/08/2013 04:29 PM

[galaxy-dev] Data library not properly showing up

Hi all, The data library I have created is only showing up partially. I have made a data libray, via het Admin menu, with one folder in it. I changed permissions, because I wanted it only to be visible to me. That worked fine. Next I created plenty more folders in that data library. Now, th

Re: [galaxy-dev] Fwd: Desire to contribute

Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/06/2013 12:08 PM, Peter Cock wrote: On Wed, Feb 6, 2013 at 11:01 AM, Joachim Jacob |VIB| wrote: In risk of getting a discussion here: a long standing enhancement request is to highlight the current history item one is

[galaxy-dev] JAVASCRIPT error - ctd.

Hi all, Occasionally, a JAVASCRIPT error appears. I think now this has to do with the app running Galaxy embedded (Fogger). This time, when I run a workflow on multiple input files (fastqc on a bunch of fastq files). The Javascript error is: ERROR updating hdas from api history contents:e

Re: [galaxy-dev] Fwd: Desire to contribute

On 02/06/2013 12:08 PM, Peter Cock wrote: On Wed, Feb 6, 2013 at 11:01 AM, Joachim Jacob |VIB| wrote: In risk of getting a discussion here: a long standing enhancement request is to highlight the current history item one is currently viewing. Situation sketch: I often hide the history items

Re: [galaxy-dev] Fwd: Desire to contribute

In risk of getting a discussion here: a long standing enhancement request is to highlight the current history item one is currently viewing. Situation sketch: I often hide the history items panel to study results (displayed in middle panel) into detail, and when I bring the history item panel

Re: [galaxy-dev] Reloading tool's configuration not working

Thanks. Yes, I am running multiple webworkers. OK, nice to know what causes this. The toolshed option will be considered. Joachim. Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/30/20

Re: [galaxy-dev] Reloading tool's configuration not working

Unfortunately, no. Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/30/2013 10:56 AM, Peter Cock wrote: On Wed, Jan 30, 2013 at 9:54 AM, Joachim Jacob |VIB| wrote: Hi, In the '

[galaxy-dev] Reloading tool's configuration not working

Hi, In the 'Admin' menu, reloading a tool's xml file does not update the tool's interface. Thanks for any assistance, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

Re: [galaxy-dev] History not updating automatically

Hi, I have a similar - but not identical issue. The history panel is not being updated: I have to restart Galaxy to see the updated panel. It appears only to happen after an error relating to the history API of Galaxy (it's a popup error, and I have closed it). My apache config (thanks f

Re: [galaxy-dev] Job manager crashes at start of Galaxy

(BITS) http://www.bits.vib.be @bitsatvib On 01/25/2013 10:13 AM, Joachim Jacob |VIB| wrote: Hi all, The jobmanager crashes when Galaxy starts. Starting server in PID 28704. Traceback (most recent call last): File "./scripts/paster.py", line 34, in command.run() File &qu

[galaxy-dev] Job manager crashes at start of Galaxy

Hi all, The jobmanager crashes when Galaxy starts. Starting server in PID 28704. Traceback (most recent call last): File "./scripts/paster.py", line 34, in command.run() File "/home/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run inv

Re: [galaxy-dev] Jobs status not being updated

.manager INFO 2013-01-24 14:05:22,524 sending stop signal to worker thread galaxy.jobs.manager INFO 2013-01-24 14:05:22,524 job manager stop queue stopped Removing PID file manager.pid Any ideas? Thanks, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34

Re: [galaxy-dev] Enhancing tool id="subtract_query1"

Thanks. Okay, I will do my first pull request. Happy that I can contribute. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 01/15/2013 11:10 AM, Joachim Jacob wrote: Hi al

Re: [galaxy-dev] JAVAscript error after initiating tool

Hi Carl, Sorry for the long delay! It did not happen in a published or shared history. But it did definitely happen in a history where some datasets where copied from another history, since I've been copying a lot lately. Thanks, J Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel:

[galaxy-dev] Jobs status not being updated

Hi all, After updating to the latest Galaxy dist-release (and moving our server to a new location - but this can not be the reason I think), the status of the jobs are not being updated. The box in the history stays grey. After restarting Galaxy or the server, the correct status of the job is

[galaxy-dev] Migration of tools

Hi, Has the devteam a schedule of the order of the tools they plan to migrate to the tool shed? Thanks, Joachim. -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib __