Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets

2014-03-14 Thread Peter Cock
On Thu, Mar 13, 2014 at 6:40 PM, Sanka, Ravi rsa...@jcvi.org wrote: I do not think so. Several individual datasets have been deleted (clicked the upper-right X on the history item box) but no History has been permanently deleted. Is there any indication in the database if target dataset or

Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output

2014-03-14 Thread Peter Cock
On Tue, Mar 4, 2014 at 12:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Mar 4, 2014 at 10:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Peter, Hello all, I've mentioned before that a forthcoming update to the BLAST+ Galaxy wrappers would be adding a most

[galaxy-dev] Quota History not getting purged

2014-03-14 Thread Alexander Kurze
Hi there, We have installed a local copy of galaxy but there seems to be a strange behavior with deleting data sets in the history panel. A few users complain that they have deleted their data sets (I can confirm that) but somehow the quota limit still doesn't show the appropriate freed space.

Re: [galaxy-dev] Quota History not getting purged

2014-03-14 Thread Peter Cock
On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze alexander.ku...@gmail.com wrote: Hi there, We have installed a local copy of galaxy but there seems to be a strange behavior with deleting data sets in the history panel. A few users complain that they have deleted their data sets (I can

Re: [galaxy-dev] Purging datasets as part of workflow?

2014-03-14 Thread John Chilton
I don't even think you can delete datasets in workflow presently - let alone permanently delete them - only hide them. https://trello.com/c/YfLGkJKe The core team just meet and a number of high priorities for the next 9 months were identified and reworking workflow scheduling was very high on

Re: [galaxy-dev] Quota History not getting purged

2014-03-14 Thread Alexander Kurze
Perfect! This solved my problem. Alex On Fri, Mar 14, 2014 at 1:23 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze alexander.ku...@gmail.com wrote: Hi there, We have installed a local copy of galaxy but there seems to be a strange

Re: [galaxy-dev] Quota History not getting purged

2014-03-14 Thread Peter Cock
On Fri, Mar 14, 2014 at 1:31 PM, Alexander Kurze alexander.ku...@gmail.com wrote: Perfect! This solved my problem. Alex That's progress. I suspect something is going wrong in the cleanup scripts failing to update the totals - but as a workaround you could include set_user_disk_usage.py as part

Re: [galaxy-dev] How To properly use GALAXY_SLOTS

2014-03-14 Thread John Chilton
I am not sure I understand what you mean, but if you are setting the job to run with a ppn of greater than one but GALAXY_SLOTS is being evaluated as 1 then you have likely uncovered a bug - maybe in the runner, your job configuration, or the GALAXY_SLOTS logic for pbs/torque. I have created a

Re: [galaxy-dev] Write permission for database/files

2014-03-14 Thread John Chilton
I did not implement this - so this is just an educated guess but I believe the relevant line of code is this: https://bitbucket.org/galaxy/galaxy-central/src/3fb927653301a0c06a0bf94f2b6bd71b3595ec0d/lib/galaxy/objectstore/__init__.py?at=default#cl-295 Hopefully someone will correct me if I am

Re: [galaxy-dev] Empty history pane

2014-03-14 Thread Liisa Koski
Thanks Dannon, I set java to open the console (I assume that's what you are referring to) but when going to galaxy it doesn't open. The console does open when i go to java.com and verify my version. i've also just removed and reinstalled java and rebooted machine. still no history pane :(

Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets

2014-03-14 Thread Peter Cock
On Fri, Mar 14, 2014 at 11:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 13, 2014 at 6:40 PM, Sanka, Ravi rsa...@jcvi.org wrote: I do not think so. Several individual datasets have been deleted (clicked the upper-right X on the history item box) but no History has been

Re: [galaxy-dev] Problem with change_format and conditional inputs?

2014-03-14 Thread John Chilton
Grepping around the code I think this is the only way a ftype attribute on an output affects the evaluation of test data. if attributes.get( 'ftype', None ) == 'bam': local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) local_name

[galaxy-dev] Verifying test output datatypes, was: Problem with change_format and conditional inputs?

2014-03-14 Thread Peter Cock
Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Note that one area of fuzziness is subclasses, e.g. if the tool output was labelled fastqsanger, but the

Re: [galaxy-dev] Dataset's extra files

2014-03-14 Thread John Chilton
The directory can be obtained using $galaxyData.extra_files_path (be sure to check it exists before zipping it up). I would discourage re-using Galaxy components directly from inside of a tool or tool wrapper - but if you want to reference that code it is actually inside of the datatypes module -

Re: [galaxy-dev] FTP password and web interface password

2014-03-14 Thread Nate Coraor
Hi Yec'han, Sorry for the delayed response - I would guess that something is different about the configuration of the SFTP server. Could you check the server logs? --nate On Thu, Mar 6, 2014 at 8:13 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi Nate, I have reseted the password of a

Re: [galaxy-dev] Job never starts

2014-03-14 Thread John Chilton
Hmm... unfortunately I have no particular guess about either of these issues. It sounds like you upgraded Galaxy and made large changes to your configuration at the same time. Can you try just one process and no load balancer so you can determine if the issue is with the Apache configuration or

Re: [galaxy-dev] Persistent jobs in cluster queue even after canceling job in galaxy

2014-03-14 Thread John Chilton
I believe this problem was fixed by Nate after the latest dist release and pushed to the stable branch of galaxy-central. https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca59825d0eb3d32afd5686c4b1b9294 If you are eager for this bug fix, you can track the latest stable branch of

Re: [galaxy-dev] How to install bowtie2 tool in galaxy

2014-03-14 Thread Nate Coraor
On Wed, Mar 5, 2014 at 8:18 PM, Ravi Alla ravi.a...@berkeley.edu wrote: Hi Jennifer, Thank you for this information. I was able to troubleshoot the bowtie2_indices. Like Bjoern said the bowtie2 tool needed to be reinstalled because the tool_table does not load the correct indices. I am still

Re: [galaxy-dev] Tool Shed install best practise : Precompiled binaries vs local compile

2014-03-14 Thread Nate Coraor
Hi Peter, I just wanted to add my $0.02 USD to say that I mostly agree with this - I have long used binaries precompiled by the tool author on Main, especially for cases where, as you say, the compile-time dependency list is large and painful. The only gotcha here is to make sure that binaries

Re: [galaxy-dev] Tool Shed install best practise : Precompiled binaries vs local compile

2014-03-14 Thread Peter Cock
On Fri, Mar 14, 2014 at 4:41 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Peter, I just wanted to add my $0.02 USD to say that I mostly agree with this - I have long used binaries precompiled by the tool author on Main, especially for cases where, as you say, the compile-time dependency list is

Re: [galaxy-dev] Tool Shed install best practise : Precompiled binaries vs local compile

2014-03-14 Thread Nate Coraor
On Fri, Mar 14, 2014 at 12:47 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Mar 14, 2014 at 4:41 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Peter, I just wanted to add my $0.02 USD to say that I mostly agree with this - I have long used binaries precompiled by the tool author on

Re: [galaxy-dev] How to install bowtie2 tool in galaxy

2014-03-14 Thread Ravi Alla
Hi Nate Thanks for the clarifications. Is there anything specific I should watch out for when updating and deleting tools? The reason I ask is that Jennifer mentioned in previous emails the need to update metadata for tools, which I am sure I follow. Thanks Ravi On Mar 14, 2014, at 9:02 AM,

Re: [galaxy-dev] Empty history pane

2014-03-14 Thread Liisa Koski
Our use was using the lastest Firefox release. I asked him to try FireFox Portable and that seemed to do the trick. It was a problem with his Firefox install. Thanks for you help, Liisa From: Dannon Baker dannon.ba...@gmail.com To: Liisa Koski liisa.ko...@basf.com Cc: Galaxy Dev

Re: [galaxy-dev] Internal server error when importing workflows!

2014-03-14 Thread John Chilton
Hmm... I can import older workflows on usegalaxy.org so I don't think it is a general problem with all workflows as a part of the latest release. That said I don't know what the problem is - if it is a bug with a new release or a problem with one of your tools etc If I had to guess I would

Re: [galaxy-dev] How To properly use GALAXY_SLOTS

2014-03-14 Thread Geert Vandeweyer
This is strange. After restarting galaxy to include the debug tool, all galaxy_slots values are correctly assigned (tested for BWA and GATK as rerun of original posted jobs) If you still need the output, let me know. Best, Geert On 03/14/2014 03:25 PM, John Chilton wrote: I am not

Re: [galaxy-dev] Empty history pane

2014-03-14 Thread Dannon Baker
Good to hear you've worked around it! For future reference, in Firefox you can open the javascript console by clicking the Firefox (menu at the top)-Web Developer-Web Console. That, or Control/Command+Shift+K. On Fri, Mar 14, 2014 at 1:49 PM, Liisa Koski liisa.ko...@basf.com wrote: Our use

Re: [galaxy-dev] Puppet Modules: a new project

2014-03-14 Thread Olivier Inizan
Dear galaxy-dev, After exchanges with Eric we have decided to create: -a common puppet module for galaxy hosted on the puppet forge: https://forge.puppetlabs.com/urgi/galaxy -a common repository hosted on a public server: We want to have the opinion of the galaxy-team and galaxy-dev community

Re: [galaxy-dev] Puppet Modules: a new project

2014-03-14 Thread John Chilton
I love this effort! I would recommend posting these on github instead of bitbucket - I think it has become kind of a puppet best practice to host collaborative repositories such as these there. For what it is worth - I have a set of puppet modules for hosting Galaxy that have a dependency on the

Re: [galaxy-dev] Persistent jobs in cluster queue even after canceling job in galaxy

2014-03-14 Thread Brian Claywell
On Fri, Mar 14, 2014 at 9:01 AM, John Chilton jmchil...@gmail.com wrote: I believe this problem was fixed by Nate after the latest dist release and pushed to the stable branch of galaxy-central. https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca59825d0eb3d32afd5686c4b1b9294 If

[galaxy-dev] Tool Testing Enhancements

2014-03-14 Thread John Chilton
Hello Tool Developers, Haven't known when to send this out, but I figure since you haven't received any e-mail from me today it might be a good time. tl;dr - Tool functional tests experienced a significant overhaul over the last release and will continue to change over the next couple releases,

Re: [galaxy-dev] Persistent jobs in cluster queue even after canceling job in galaxy

2014-03-14 Thread Ravi Alla
What are the best practices for updating galaxy? Also is there a quick command I can run to see what version of galaxy I am running? On Mar 14, 2014, at 12:23 PM, Brian Claywell bclay...@fhcrc.org wrote: On Fri, Mar 14, 2014 at 9:01 AM, John Chilton jmchil...@gmail.com wrote: I believe this

Re: [galaxy-dev] Verifying test output datatypes, was: Problem with change_format and conditional inputs?

2014-03-14 Thread John Chilton
On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John, I suggest making this test framework perform this check by default (the twill and API based frameworks) and seeing what - if anything - breaks as a result on the Test Tool Shed. Hey Peter, I hope it