Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy

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Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy

Nate Coraor (nate@bx.psu.edu)
Hi Rodolfo,

I've moved this over to the galaxy-dev list since it's a local
installation issue.

Rodolfo Aramayo wrote:

> People,
>
> Apologies for the disturbance.
>
> On a fresh MacOSX I installed Python, Numpy and Scipy using MacPorts
>
> I tested both Numpy and Scipy as follows:
>
> ==
>    python
>    >>> import numpy
>    >>> numpy.test('1','10')
>    >>> import scipy
>    >>> scipy.test('1','10')
> ==
>
> The computer does understand them and processes them as expected. The
> tests seem to work?
>
> However, when I attempt a fresh installation of Galaxy I get the
> following error:
>
>> hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
> requesting all changes
> adding changesets
> adding manifests
> adding file changes
> added 3787 changesets with 17203 changes to 4176 files
> updating to branch default
> 2691 files updated, 0 files merged, 0 files removed, 0 files unresolved
>
>> sh setup.sh
> Copying datatypes_conf.xml.sample to datatypes_conf.xml
> Copying reports_wsgi.ini.sample to reports_wsgi.ini
> Copying tool_conf.xml.sample to tool_conf.xml
> Copying universe_wsgi.ini.sample to universe_wsgi.ini
> Copying tool-data/alignseq.loc.sample to tool-data/alignseq.loc
> Copying tool-data/annotation_profiler_options.xml.sample to
> tool-data/annotation_profiler_options.xml
> Copying tool-data/annotation_profiler_valid_builds.txt.sample to
> tool-data/annotation_profiler_valid_builds.txt
> Copying tool-data/binned_scores.loc.sample to tool-data/binned_scores.loc
> Copying tool-data/blastdb.loc.sample to tool-data/blastdb.loc
> Copying tool-data/bowtie_indices.loc.sample to tool-data/bowtie_indices.loc
> Copying tool-data/encode_datasets.loc.sample to tool-data/encode_datasets.loc
> Copying tool-data/liftOver.loc.sample to tool-data/liftOver.loc
> Copying tool-data/maf_index.loc.sample to tool-data/maf_index.loc
> Copying tool-data/maf_pairwise.loc.sample to tool-data/maf_pairwise.loc
> Copying tool-data/microbial_data.loc.sample to tool-data/microbial_data.loc
> Copying tool-data/phastOdds.loc.sample to tool-data/phastOdds.loc
> Copying tool-data/quality_scores.loc.sample to tool-data/quality_scores.loc
> Copying tool-data/regions.loc.sample to tool-data/regions.loc
> Copying tool-data/sam_fa_indices.loc.sample to tool-data/sam_fa_indices.loc
> Copying tool-data/sequence_index_base.loc.sample to
> tool-data/sequence_index_base.loc
> Copying tool-data/sequence_index_color.loc.sample to
> tool-data/sequence_index_color.loc
> Copying tool-data/twobit.loc.sample to tool-data/twobit.loc
> Copying tool-data/shared/ucsc/builds.txt.sample to
> tool-data/shared/ucsc/builds.txt
> Creating database/files
> Creating database/community_files
> Creating database/tmp
> Creating database/compiled_templates
> Creating database/job_working_directory
> Creating database/pbs
> Creating static/genetrack/plots
> Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.6.egg
> Fetched http://eggs.g2.bx.psu.edu/new/docutils/docutils-0.4-py2.6.egg
> Traceback (most recent call last):
>   File "./scripts/fetch_eggs.py", line 31, in <module>
>     c.resolve() # Only fetch eggs required by the config
>   File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py",
> line 284, in resolve
>     egg.resolve()
>   File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py",
> line 172, in resolve
>     r = pkg_resources.working_set.resolve( (
> self.distribution.as_requirement(), ), env, self.fetch )
>   File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py",
> line 551, in resolve
>     raise DistributionNotFound(req)
> pkg_resources.DistributionNotFound: numpy==1.3.0
> Any Ideas?

Galaxy is not directly supported on MacPorts Python, since that version
isn't (or wasn't, previously) a "fat" (multiplatform) Framework build.
The Apple system-provided Python in Leopard and Snow Leopard, as well as
the official releases from python.org are all supported.

You may be able to use the MacPorts version by building your own Python
Eggs.  I'd try first with numpy:

% python scripts/scramble.py numpy

And see if that works.

--nate

>
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> http://lists.bx.psu.edu/listinfo/galaxy-user
>

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Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy

Modi, Amit
Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy
Hi,

I created a few conditional cases  in the xml file for taking input for my tool.

I added two values to a list and based on the values the rest of the interface is generated.

This works fine when I do this for a simple list but does not to work well when I changed the list to radio button.

Does any one knows how to get this working.

Thanks a lot.

Regards,
Amit Modi
 


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