Re: [galaxy-dev] import Workflow from public Galaxy to local instance

. regards, Andreas On 22.05.2013 13:57, Dannon Baker wrote: On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/__gm2123/w

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

, Andreas -Dannon On Tue, May 21, 2013 at 11:56 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: Hi, I want to make workflows published on usegalaxy.org http://usegalaxy.org available for users on our local instance. How do I do

[galaxy-dev] how to set GridEngine parameters for tools

tool id=velveth destination=cluster/ /tools ... But where do I put the -l h_vmem? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http

Re: [galaxy-dev] how to set GridEngine parameters for tools

velveth = drmaa://-l h_vmem=25G/ In the new style I would write ... destinations destination id=cluster runner=drmaa/ /destinations tools tool id=velveth destination=cluster/ /tools ... But where do I put the -l h_vmem? regards, Andreas -- Andreas Kuntzagk

[galaxy-dev] import Workflow from public Galaxy to local instance

Hi, I want to make workflows published on usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str

[galaxy-dev] error when looking at tool error

, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

Re: [galaxy-dev] Permission denied error for velveth

cheetah_DynamicallyCompiledCheetahTemplate_1354790596_63_67504.py, line 84, in respond NotFound: cannot find 'files_path' while searching for 'input.files_path' Andreas On 06.12.2012 10:52, Andreas Kuntzagk wrote: Sorry, I think I had not really restarted galaxy after making the change. After I

[galaxy-dev] Permission denied error for velveth

-- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

Re: [galaxy-dev] multithreaded tools

processes started for a galaxy lastz job must involve post-processing the lastz output through some other shell tool. Lastz by itself doesn't support multiple threads or processes. Bob H On Nov 26, 2012, at 3:58 AM, Andreas Kuntzagk wrote: Hi, I'm wandering how galaxy supports tools

Re: [galaxy-dev] multithreaded tools

to request that many slots/CPUs. A list of all these wrappers on the Wiki would be nice. regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http

Re: [galaxy-dev] multithreaded tools

Andreas Kuntzagk Verzonden: dinsdag 27 november 2012 9:58 Aan: Bob Harris CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] multithreaded tools Hi, the four processes I saw where all called lastz and ran in parallel and consumed 100% of a core each. My guess

Re: [galaxy-dev] multithreaded tools

Hi Peter, thanks for your replies. On 27.11.2012 11:44, Peter Cock wrote: On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Dear Peter, As the author of several tool wrappers, I've been asking for a Galaxy wide mechanism for Galaxy to tell the tool how

[galaxy-dev] How to delete a toolshed tool completely or change category

. Is there a way to really uninstall? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

Re: [galaxy-dev] How to delete a toolshed tool completely or change category

Please ignore this. You can move it to a different section. Andreas On 27.11.2012 13:19, Andreas Kuntzagk wrote: Hi, In the past I installed bwa_wrapper from the toolshed. Unfortunately I must have choosen a wrong category. Currently it is not part of any tool section. According

Re: [galaxy-dev] lastz on local galaxy failing

can try running this via the console, and see if there's something happening in lastz that I don't understand? Bob H On Nov 26, 2012, at 3:35 AM, Andreas Kuntzagk wrote: Hi, I just noticed that this was another case of a tool that needs more then the 1GB memory that is default on our cluster

Re: [galaxy-dev] lastz on local galaxy failing

Hi, I just noticed that this was another case of a tool that needs more then the 1GB memory that is default on our cluster. After adjusting the job_runner settings everything seems fine. regards, Andreas On 15.11.2012 09:08, Andreas Kuntzagk wrote: Hi, when I start a lastz job it submits

[galaxy-dev] multithreaded tools

Hi, I'm wandering how galaxy supports tools that are multithreaded or multi-process. When working with lastz I noticed that it starts 4 parallel processes. Is that always so? Can this be adjusted? What other tools also are multi-process? regards, Andreas -- Andreas Kuntzagk

[galaxy-dev] lastz on local galaxy failing

; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0 galaxy.jobs.runners.drmaa INFO 2012-11-15 09:03:11,553 (254) queued as 1282605 galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:11,767 (254/1282605) state change: job is running -- Andreas Kuntzagk SystemAdministrator Berlin Institute

[galaxy-dev] tool_id for tool_shed tools

Hi, I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over the tool name and write down the id? regards, Andreas -- Andreas Kuntzagk

Re: [galaxy-dev] hg18.fa on rsync? [was: which .loc file for SAM to BAM?]

Ok, I've found the solution. sam_fa_indices.loc contained relative paths. When I changed to absolute paths it worked. regards, Murple On 02.11.2012 09:26, Andreas Kuntzagk wrote: Oh, I forgot to mention it: hg18.fa.fai is already in tool-data/shared/ucsc/hg18/sam_index/ as a link to tool

Re: [galaxy-dev] hg18.fa on rsync? [was: which .loc file for SAM to BAM?]

, Andreas Kuntzagk wrote: Dave, In the meantime I found that out by myself howto generate the FASTA and also to rum samtools faidx on it. The info about all_fasta.loc was missing. But it's still not working. Let me summarize what I did so far: - tool-data/shared/ucsc/hg18/seq/ contains

Re: [galaxy-dev] which .loc file for SAM to BAM?

Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc

[galaxy-dev] hg18.fa on rsync? [was: which .loc file for SAM to BAM?]

, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try SAM to BAM for a BAM file that has hg18 set as build I get a message that Sequences are not currently available

Re: [galaxy-dev] hg18.fa on rsync? [was: which .loc file for SAM to BAM?]

the relevant .2bit file and converting it back to FASTA with twoBitToFa, then updating your all_fasta.loc file to point to the resulting .fa file. --Dave B. On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote: Hi, It's still not working. I just noticed that the sam_index dir only contains links

Re: [galaxy-dev] which .loc file for SAM to BAM?

be added to the page you are mentioning. On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards

[galaxy-dev] which .loc file for SAM to BAM?

? These lines seem very redundant to me. -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

[galaxy-dev] Error when creating Visualization

-py2.6.egg/sqlalchemy/orm/attributes.py', line 847 in set new_state, new_dict = instance_state(child), instance_dict(child) AttributeError: 'dict' object has no attribute '_sa_instance_state' Any idea what may be wrong? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin

Re: [galaxy-dev] Error when creating Visualization

My fault. I did not set a title for it. (Anyway this should be caught I think.) regards, Andreas On 25.10.2012 13:18, Andreas Kuntzagk wrote: Hi, on our local Galaxy instance I try to setup Visualization. I followed http://wiki.g2.bx.psu.edu/Learn/Visualization#Setup_for_Local_Instances

Re: [galaxy-dev] renaming fastq to fastqsanger

Dartmouth College, HB 6223 L24 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 http://discovery.dartmouth.edu http://columbia.dartmouth.edu/grid http://www.epistasis.org * This body part will be downloaded on demand. -- Andreas Kuntzagk SystemAdministrator Berlin Institute

[galaxy-dev] Which bam_to_bigwig to use

In the main toolshed I find bam_to_bigwig 2 times. Description, Version and Requirements seem the same. How am I to decide which one to use? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine

[galaxy-dev] problem with data libraries

'. What is the problem here? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

Re: [galaxy-dev] run cluster jobs as real user

I'm sure there are some bugs. regards, Andreas On 29.03.2012 16:12, Andreas Kuntzagk wrote: Hi, Ok, I was digging around for this and it seems to be a bit more involved then I expected. Problem is I don't really understand the interplay of DRMAAJobRunner and the user management. Can somebody

Re: [galaxy-dev] run cluster jobs as real user

. For unknown users I just continue to use the galaxy user. I guess a good starting point would be DRMAAJobRunner.queue_job Do you see any bigger problems coming my way? How best do I avoid to degress from the main tree to much? regards, Andreas On 27.03.2012 09:57, Andreas Kuntzagk wrote: Hi

Re: [galaxy-dev] run cluster jobs as real user

. On 20/03/12 16:31, Andreas Kuntzagk wrote: Hi, I (re-)installed galaxy on our server and managed to set it up to run jobs through our cluster (GridEngine). It's also running behind an Apache proxy now. But now I'm wondering how to setup to have the cluster jobs run as the real cluster users. I

[galaxy-dev] login not working on local instance

to # be created by an admin). #allow_user_creation = True # Allow administrators to delete accounts. #allow_user_deletion = False # Allow administrators to log in as other users (useful for debugging) #allow_user_impersonation = False regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin

[galaxy-dev] run cluster jobs as real user

a little thin. We use NIS for managing users and passwords across the cluster. How do I connect that to Galaxy? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125