Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy
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
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
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 ----------------------------------------- Confidentiality Notice: The following mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. The recipient is responsible to maintain the confidentiality of this information and to use the information only for authorized purposes. If you are not the intended recipient (or authorized to receive information for the intended recipient), you are hereby notified that any review, use, disclosure, distribution, copying, printing, or action taken in reliance on the contents of this e-mail is strictly prohibited. If you have received this communication in error, please notify us immediately by reply e-mail and destroy all copies of the original message. Thank you.
participants (2)
-
Modi, Amit -
Nate Coraor