- galaxy-dev - lists.galaxyproject.org

Error filtering sam files
by Juan Vladimir de la Rosa Medina 21 Mar '16

21 Mar '16

Hi guys, when I try to run "Filter SAM or BAM, output SAM or BAM" from SAMtools on our local galaxy instance, we get this error: Traceback (most recent call last): File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job job_wrapper.prepare() File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/jobs/__init__.py", line 889, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/jvdelarosa/Bioinformatica/Software/galaxy/lib/galaxy/tools/evaluation.py", line 442, in build raise e ValueError: invalid literal for int() with base 16: '' Enviado desde Correo para Windows 10

1 0

per-tool job resource defaults
by Stephan Oepen 21 Mar '16

21 Mar '16

dear colleagues, at the university of oslo, we develop a galaxy-based portal for natural language processing (LAP: Language Analysis Portal). jobs are submitted to a compute cluster via DRMAA and SLURM. current development is against the galaxy release of march 2015. i am wondering about fine-grained control of job resources. our goal is that most users need not look past the ‘Use default job resource parameters’ toggle in the job configuration dialogue. as i understand it, i think we can populate the ‘nativeSpecification’ parameter in ‘job_conf.xml’ with SLURM-specific command-line options to set defaults, for example the project, maximum run-time, number of cores, memory per core, and such. i assume these defaults will be combined with and overwritten by ‘custom’ job resource parameters, in case any are specified in the job configuration dialogue? i tried to track the flow of information from ‘lib/galaxy/jobs/runners/drmaa.py’ via ‘scripts/drmaa_external_runner.py’ into the drmaa-python egg, but i could not easily work out where the merging of ‘nativeSpecification’ and custom resource parameters happens; presumably at about the same time as an actual job script file is created, for submission to SLURM? could someone point me in the right direction here? —more importantly, maybe: we would like to establish per-tool resource defaults. for example, some of our tools require substantially more memory per core than others. i cannot easily find a way of associating resource default with individual tools. i looked at the tool configuration syntax, ‘job_conf.xml.sample_advanced’, and ‘job_resource_params_conf.xml.sample’, as well as at the following documentation pages: https://wiki.galaxyproject.org/Admin/Config/Jobs https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster i am hoping i am overlooking something :-). is there a way to define job resource defaults on a per-tool basis? with warmest thanks in advance, oe

3 4

Problem with tool dependency
by Mikael Loaec 21 Mar '16

21 Mar '16

Hi, We, actually have problems with installation of some tools using the galaxy web interface or the API throught the script install_tool_shed_tools.py ( https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/ins… ). When a tool has a package dependency, the dependency is installed, but the env.sh of this dependency is not sourced at the end of its installation and before the installation of the parent tool. So the dependency is installed, but the parent tool installation failed because it needs the env.sh of the depency sourced. For example for GATK : When we install GATK, it looks up for R, which is installed correctly but its path is not sourced so GATK installation failled. Any idea ? Do we have a problem in our configuration or it's a known problem ? Thanks in Advance for your response. Regards, Mikael & Françoise URGI INRA

1 0

planemo update failing on testtoolshed
by Peter van Heusden 18 Mar '16

18 Mar '16

Hi there I'm trying to update a newly created tool on the test tool shed and I get this error: $ planemo shed_update -t testtoolshed cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet Could not update split_fasta_chunks Unexpected response from galaxy: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> Repository metadata updated. Failed to update a repository. I might have accidentally created a "bad" repository that is leading to this error. This is with version 0.23.0. Alternately, is there a way to delete the tool so that I can try and recreate it? Thanks! Peter

2 2

removing tool from toolshed
by Xianrong Wong 18 Mar '16

18 Mar '16

Hi, I've recently packaged some of my scripts and deposited them into the test toolshed. Are there ways to remove some of them ie remove the repository completely? Jose

2 1

Cloudman & AWS IAM_PROFILE support?
by Ryan G 17 Mar '16

17 Mar '16

Hi - Does Cloudman support IAM_PROFILES? We run our instances within a VPC and assign an IAM_PROFILE to the ec2 instances so that they have access to resouces. Does Cloudman have this support?

3 6

Test tool shed api - repositories.get_ordered_installable_revisions() not working?
by Simon Gladman 17 Mar '16

17 Mar '16

Hi all, I've been trying to access the test tool shed via the bioblend api. It keeps failing when I try to call get_ordered_installable_revisions() on a connection to it. Is anyone else having this problem. Please find a jupyter screenshot where I have replicated this problem. It all works fine on the main toolshed. [image: Inline images 1] -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 700 Swanston Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

2 2

Re: [galaxy-dev] Please help fix toolshed repository: trtr
by Martin Čech 17 Mar '16

17 Mar '16

Hi Lance, Dave Bouvier removed the unwanted folder on the TS side. (It wasn't ever tracked by mercurial). You should be ok now. Sorry for the inconvenience. Thank you for using Galaxy. Martin On Tue, Mar 15, 2016 at 5:41 PM Lance Parsons <lparsons(a)princeton.edu> wrote: > When I clone the repo, I don't see that folder: > > hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr > > Lance > > Martin Čech wrote: > > > Hi Lance, > > it seems the whole .git/ folder got accidentally uploaded there and it > causes trouble. I recommend using the direct mercurial access > (https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr) delete the > folder, commit the change and push it to the TS repository. > > Please let me know how it goes. > > Martin > > On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons <lparsons(a)princeton.edu > > <mailto:lparsons@princeton.edu>> wrote: > > I was helping someone with their toolshed repository and we ran > into an issue, there is an old folder "myTools" in the repository > that we cannot delete. It has a second copy of the tool > (inadvertently). However, when we upload a new version with > Planemo, the directory remains. Attempts to delete it via the > toolshed web interface result in internal server errors. Can an > admin take a look? > > https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301 > > > -- > Lance Parsons - Scientific Programmer > Carl C. Icahn Laboratory - Room 136 > Lewis-Sigler Institute for Integrative Genomics > Princeton University > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > >

1 0

Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)
by Dooley, Damion 17 Mar '16

17 Mar '16

If you are looking for a simple python program to log cpu% and memory of another executable, then analyze.py might do. Its in https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test -case along with a few scripts that show examples of its use. Damion >> >> On 02/21/2016 11:13 PM, Peter van Heusden wrote: >> >> Hi there >> >> We're researching the resource (CPU time and memory) requirements for >>RNA >> STAR at the moment. Specifically, we'd like to build up a database of >>input >> size to resource usage so that we can use this to feed a dynamic >> destination mapper (currently our STAR configuration uses a thumbsuck >>for >> RAM and CPU requirements that is not optimal but works in many cases). >> >> Has anyone collected these metrics before? And more generally, is anyone >> collecting metrics for a range of bioinformatics tools? A database like >> this could be very useful! >> >> Thanks! >> Peter >>

2 1

Announcement: Galaxy DevOps Workshop
by Bjoern Gruening 17 Mar '16

17 Mar '16

Hi all, We would like to invite you to our Galaxy DevOps Workshop in Heidelberg from 6-7 of April, organised by de.NBI and ELIXIR. The workshop is intended for Bioinformaticians who want to * learn the internals of the multi-omics Galaxy workbench * learn how to set up and run a Galaxy server * learn about Galaxy tool development * get questions answered from experienced Galaxy admins and community members * are interested in reproducible and accessible research For more information please see https://goo.gl/8dNSdy Ciao, Bjoern

1 0