Re: [galaxy-dev] samtools installation problems

Thank you all for the help! Its all running smoothly now. Best, Nathan On Wed, Dec 31, 2014 at 3:50 PM, Björn Grüning wrote: > Hi Nathan, > > please try the following. > > ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/ > /path/to/your/shed_tools/samttools/default > > The impo

[galaxy-dev] Problem using FastQC in Galaxy

Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this: # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_wo

Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?

Hi John, I did some investigation. I added logging statement to line 843 of lib/galaxy/workflow/modules.py file: for step in workflow.steps: step_args = param_map.get( step.id, {} ) * log.info ('step.id =' + str(step.id ) + ', step_a

Re: [galaxy-dev] [Spam:*****] Re: How galaxy workflow work ?

galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator rval = func( self, trans, *args, **kwargs) File "/home/ga

[galaxy-dev] visualization in anonymous mode ?

Hi, I'd like to use the visualization in anonymous mode, but the visualize icon on the dataset is not available in anonymous mode (although it works fine when connected). Is it possible to activate the dataset visualization in anonymous mode ? Thanks, Loraine -- Loraine Guéguen Plateform

[galaxy-dev] bx_python_0_7 installation error

Hi, Björn, thanks for your tip. I am working on SLES11. After installing LAPACK and ATLAS, I could install numpy1.7.1 by using Galaxy main tool shed. But installation of bx_python_0_7 produced a new error message: bx-python

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Hi, Björn, my intention was to test a simple workflow (BASIC PROTOCOL 1 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418382/) on my local galaxy installation. By default, “join” function is not installed on galaxy. When I tried to install “join”, it reported error on the installation of bx_pytho

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Hi Wang, can you point me to the exact version your try to install. There is an old numpy_1_7 package which should be deprecated. We had a lot of trouble installing ATLAS and LAPACK and decided to deprecate all packages which depends on LAPACK and ATLAS. Now we do not require both libraries anymor

[galaxy-dev] Create a package with binaries

Hi gentlemen, I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message: mytool.sh: line 14: mytool: unknown command It seems that t

[galaxy-dev] galaxy.tools.parameters.basic.RuntimeValue not str

Hi all! Maybe somebody faced with this problem: 1) in my wf used tool with: "u'model_class': u'Conditional', u'type': u'conditional', u'name': u'reference_genome'}], " 2) when i run wf via web - all ok, and on a second step: "Select a reference genome" is "test" (in view details) But,