Problems Installing Galaxy

Question: Problems Installing Galaxy

8.5 years ago by

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: 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 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/__ini t__.py", line 284, in resolve egg.resolve() File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__ini t__.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/li b/python2.6/site-packages/pkg_resources.py", line 551, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: numpy==1.3.0 Any Ideas?

alignment bowtie • 1.0k views

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modified 7.0 years ago by Dave Clements ♦♦ 2.5k • written 8.5 years ago by Rodolfo Aramayo • 30

7.0 years ago by

Dave Clements ♦♦ 2.5k

United States

Dave Clements ♦♦ 2.5k wrote:

Dear Gretel, I am copying this question to the Galaxy-User mailing list, which is the best place to discuss it. Also, see http://galaxyproject.org/wiki/Supportfor other ways to get information. Can you post some additional information to this thread? In particular: * What steps are missing from the histories? Do the steps have anything in common? * Are you trying to view histories that were created on, and have always been stored, on the public Galaxy list; or are you loading a history into that server that was exported from another Galaxy Server? Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

ADD COMMENT • link written 7.0 years ago by Dave Clements ♦♦ 2.5k

Hi Gretel, I just read the rest of my inbox. It appears that you are not the only person experiencing problems with the history panel today. Someone from Galaxy will get back to you once we have this figured out. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

ADD REPLY • link written 7.0 years ago by Dave Clements ♦♦ 2.5k

Hello Gretel, There was a temporary problem that has now been resolved. The History panel should now load as expected. Jobs will also be started, however the time to start and will likely be longer than usual due to many users starting their jobs at the same time. Very sorry for any inconvenience, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

ADD REPLY • link written 7.0 years ago by Jennifer Hillman Jackson ♦ 25k

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