Re: [galaxy-dev] [galaxy-user] Error running latest Galaxy Distribution: numpy.dtype exception
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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Hi Nate,
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
$ python ./scripts/get_platforms.py macosx-10.6-universal-ucs2 $ python -V Python 2.6.1
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
Just in case it helps:
I'm currently running tip of galaxy-dist:
hg tip changeset: 5585:8c11dd28a3cf tag: tip user: Nate Coraor nate@bx.psu.edu date: Thu May 19 10:07:53 2011 -0400 summary: Add Picard and fastqc tools to Main
My prior version which is still working for me is:
changeset: 5355:50e249442c5a user: Daniel Blankenberg dan@bx.psu.edu date: Thu Apr 07 08:39:07 2011 -0400 summary: Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
~Mike
What is the version for numpy in your eggs.ini?
On Wed, Jun 15, 2011 at 3:14 PM, Michael Steder steder@ci.uchicago.eduwrote:
Hi Nate,
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
$ python ./scripts/get_platforms.py macosx-10.6-universal-ucs2 $ python -V Python 2.6.1
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
Just in case it helps:
I'm currently running tip of galaxy-dist:
hg tip changeset: 5585:8c11dd28a3cf tag: tip user: Nate Coraor nate@bx.psu.edu date: Thu May 19 10:07:53 2011 -0400 summary: Add Picard and fastqc tools to Main
My prior version which is still working for me is:
changeset: 5355:50e249442c5a user: Daniel Blankenberg dan@bx.psu.edu date: Thu Apr 07 08:39:07 2011 -0400 summary: Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
~Mike
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:
On Jun 15, 2011, at 3:36 PM, Kanwei Li wrote:
What is the version for numpy in your eggs.ini?
eggs.ini has "numpy = 1.3.0". I have no local edits this is just a clean checkout of galaxy-dist.
~Mike
On Wed, Jun 15, 2011 at 3:14 PM, Michael Steder steder@ci.uchicago.edu wrote: Hi Nate,
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
$ python ./scripts/get_platforms.py macosx-10.6-universal-ucs2 $ python -V Python 2.6.1
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
Just in case it helps:
I'm currently running tip of galaxy-dist:
hg tip changeset: 5585:8c11dd28a3cf tag: tip user: Nate Coraor nate@bx.psu.edu date: Thu May 19 10:07:53 2011 -0400 summary: Add Picard and fastqc tools to Main
My prior version which is still working for me is:
changeset: 5355:50e249442c5a user: Daniel Blankenberg dan@bx.psu.edu date: Thu Apr 07 08:39:07 2011 -0400 summary: Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
~Mike
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:
Any other ideas? I can run galaxy-central but I'd like to work with the stable galaxy if possible.
Because earlier revs of galaxy-dist startup fine for me I went through the exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585 as bad I went through some revs, each time attempting to start the server. The bad revs failed to startup with ValueError 'numpy.dtype' exception where the good revs started fine.
So according to hg bisect:
The first bad revision is: changeset: 5410:0194ab30a730 user: Nate Coraor nate@bx.psu.edu date: Mon Apr 18 16:42:12 2011 -0400 summary: Update bx-python to the tip.
I'm not sure from the diff what change in that revision could cause this error.
What am I missing? Is anyone else having trouble running the latest galaxy-dist?
~Mike
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Michael Steder wrote:
Any other ideas? I can run galaxy-central but I'd like to work with the stable galaxy if possible.
I can rebuild the bx_python egg, but it's odd this is happening - the old numpy eggs haven't changed in over a year. Could you remove ~/.python-eggs, and the bx_python and numpy eggs from Galaxy's eggs/ subdirectory, and then try again?
Thanks, --nate
Because earlier revs of galaxy-dist startup fine for me I went through the exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585 as bad I went through some revs, each time attempting to start the server. The bad revs failed to startup with ValueError 'numpy.dtype' exception where the good revs started fine.
So according to hg bisect:
The first bad revision is: changeset: 5410:0194ab30a730 user: Nate Coraor nate@bx.psu.edu date: Mon Apr 18 16:42:12 2011 -0400 summary: Update bx-python to the tip.
I'm not sure from the diff what change in that revision could cause this error.
What am I missing? Is anyone else having trouble running the latest galaxy-dist?
~Mike
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
I tried the following:
$ rm -rf ~/.python-eggs/ $ cd galaxy-dist $ rm -f ~/eggs/* $ sh run.sh Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx... Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Cheetah/Cheetah-2.2.2-py2.6-macosx-10.6-universal-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.0_494c2d1d68b3-py2.6-macos... Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.3.0-py2.6-macosx-10.6-universal-ucs2... Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-macosx... Fetched http://eggs.g2.bx.psu.edu/Beaker/Beaker-1.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/SVGFig/SVGFig-1.1.6-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/SQLAlchemy/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.6-macosx-10.6-univ... Fetched http://eggs.g2.bx.psu.edu/NoseTestDiff/NoseTestDiff-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.6-macos... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/MarkupSafe/MarkupSafe-0.12-py2.6-macosx-10.6-unive... Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Routes/Routes-1.12.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0ca... Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.6-macosx-10.6-universa... Fetched http://eggs.g2.bx.psu.edu/WebError/WebError-0.8a-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Paste/Paste-1.6-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.6.... Fetched http://eggs.g2.bx.psu.edu/WebOb/WebOb-0.8.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteScript/PasteScript-1.7.3-py2.6.egg Fetch successful. Traceback (most recent call last): File "/Users/steder/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
:-/
~Mike
On Jun 16, 2011, at 9:29 AM, Nate Coraor wrote:
Michael Steder wrote:
Any other ideas? I can run galaxy-central but I'd like to work with the stable galaxy if possible.
I can rebuild the bx_python egg, but it's odd this is happening - the old numpy eggs haven't changed in over a year. Could you remove ~/.python-eggs, and the bx_python and numpy eggs from Galaxy's eggs/ subdirectory, and then try again?
Thanks, --nate
Because earlier revs of galaxy-dist startup fine for me I went through the exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585 as bad I went through some revs, each time attempting to start the server. The bad revs failed to startup with ValueError 'numpy.dtype' exception where the good revs started fine.
So according to hg bisect:
The first bad revision is: changeset: 5410:0194ab30a730 user: Nate Coraor nate@bx.psu.edu date: Mon Apr 18 16:42:12 2011 -0400 summary: Update bx-python to the tip.
I'm not sure from the diff what change in that revision could cause this error.
What am I missing? Is anyone else having trouble running the latest galaxy-dist?
~Mike
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Michael Steder wrote:
I tried the following:
$ rm -rf ~/.python-eggs/ $ cd galaxy-dist $ rm -f ~/eggs/* $ sh run.sh Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx... Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Cheetah/Cheetah-2.2.2-py2.6-macosx-10.6-universal-... Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/bx_python/bx_python-0.7.0_494c2d1d68b3-py2.6-macos... Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/numpy/numpy-1.3.0-py2.6-macosx-10.6-universal-ucs2... Fetched http://eggs.g2.bx.psu.edu/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-macosx... Fetched http://eggs.g2.bx.psu.edu/Beaker/Beaker-1.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/SVGFig/SVGFig-1.1.6-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/SQLAlchemy/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/simplejson/simplejson-2.1.1-py2.6-macosx-10.6-univ... Fetched http://eggs.g2.bx.psu.edu/NoseTestDiff/NoseTestDiff-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/python_lzo/python_lzo-1.08_2.03_static-py2.6-macos... Fetched http://eggs.g2.bx.psu.edu/wchartype/wchartype-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/MarkupSafe/MarkupSafe-0.12-py2.6-macosx-10.6-unive... Fetched http://eggs.g2.bx.psu.edu/twill/twill-0.9-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Routes/Routes-1.12.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/elementtree/elementtree-1.2.6_20050316-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/decorator/decorator-3.1.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/GeneTrack/GeneTrack-2.0.0_beta_1_dev_48da9e998f0ca... Fetched http://eggs.g2.bx.psu.edu/pycrypto/pycrypto-2.0.1-py2.6-macosx-10.6-universa... Fetched http://eggs.g2.bx.psu.edu/WebError/WebError-0.8a-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Paste/Paste-1.6-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/wsgiref/wsgiref-0.1.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/python_daemon/python_daemon-1.5.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/nose/nose-0.11.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.6.... Fetched http://eggs.g2.bx.psu.edu/WebOb/WebOb-0.8.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteScript/PasteScript-1.7.3-py2.6.egg Fetch successful. Traceback (most recent call last): File "/Users/steder/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
:-/
Arright, I'm running out of ideas, the same platform and python version on a fresh checkout works fine for me and the other developers.
Could you remove just your bx_python egg and then scramble it locally:
% rm -rf eggs/bx_python* % python ./scripts/scramble.py bx_python
Sorry for all the hassle, --nate
~Mike
On Jun 16, 2011, at 9:29 AM, Nate Coraor wrote:
Michael Steder wrote:
Any other ideas? I can run galaxy-central but I'd like to work with the stable galaxy if possible.
I can rebuild the bx_python egg, but it's odd this is happening - the old numpy eggs haven't changed in over a year. Could you remove ~/.python-eggs, and the bx_python and numpy eggs from Galaxy's eggs/ subdirectory, and then try again?
Thanks, --nate
Because earlier revs of galaxy-dist startup fine for me I went through the exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585 as bad I went through some revs, each time attempting to start the server. The bad revs failed to startup with ValueError 'numpy.dtype' exception where the good revs started fine.
So according to hg bisect:
The first bad revision is: changeset: 5410:0194ab30a730 user: Nate Coraor nate@bx.psu.edu date: Mon Apr 18 16:42:12 2011 -0400 summary: Update bx-python to the tip.
I'm not sure from the diff what change in that revision could cause this error.
What am I missing? Is anyone else having trouble running the latest galaxy-dist?
~Mike
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Jun 16, 2011, at 9:55 AM, Nate Coraor wrote:
Arright, I'm running out of ideas, the same platform and python version on a fresh checkout works fine for me and the other developers.
Could you remove just your bx_python egg and then scramble it locally:
% rm -rf eggs/bx_python* % python ./scripts/scramble.py bx_python
Sorry for all the hassle, --nate
It's not too much hassle, I just wanted to be sure I could run galaxy-dist before upgrading my working repo.
Nate, that worked. Thanks for the help!
~Mike
~Mike
On Jun 16, 2011, at 9:29 AM, Nate Coraor wrote:
Michael Steder wrote:
Any other ideas? I can run galaxy-central but I'd like to work with the stable galaxy if possible.
I can rebuild the bx_python egg, but it's odd this is happening - the old numpy eggs haven't changed in over a year. Could you remove ~/.python-eggs, and the bx_python and numpy eggs from Galaxy's eggs/ subdirectory, and then try again?
Thanks, --nate
Because earlier revs of galaxy-dist startup fine for me I went through the exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585 as bad I went through some revs, each time attempting to start the server. The bad revs failed to startup with ValueError 'numpy.dtype' exception where the good revs started fine.
So according to hg bisect:
The first bad revision is: changeset: 5410:0194ab30a730 user: Nate Coraor nate@bx.psu.edu date: Mon Apr 18 16:42:12 2011 -0400 summary: Update bx-python to the tip.
I'm not sure from the diff what change in that revision could cause this error.
What am I missing? Is anyone else having trouble running the latest galaxy-dist?
~Mike
On Jun 15, 2011, at 12:18 PM, Nate Coraor wrote:
Michael Steder wrote:
I'm just following the documentation here: https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy
And I ran into the following error:
$ hg clone https://bitbucket.org/galaxy/galaxy-dist $ cd galaxy-dist $ sh run.sh Fetch successful. Traceback (most recent call last): File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 81, in app_factory from galaxy.app import UniverseApplication File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/app.py", line 11, in <module> from galaxy.tools.imp_exp import load_history_imp_exp_tools File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/tools/imp_exp/__init__.py", line 6, in <module> from galaxy.web.base.controller import UsesHistory File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/web/base/controller.py", line 12, in <module> from galaxy.visualization.tracks.data_providers import get_data_provider File "/Users/steder/GO/GoGalaxy/galaxy-dist/lib/galaxy/visualization/tracks/data_providers.py", line 16, in <module> from bx.arrays.array_tree import FileArrayTreeDict File "numpy.pxd", line 119, in init bx.arrays.array_tree (lib/bx/arrays/array_tree.c:11323) ValueError: numpy.dtype does not appear to be the correct type object
I was able to run the previous stable version of Galaxy. Is there something I can do to get galaxy-dist running?
Hi Mike,
I'm moving this over to galaxy-dev since it deals with a local installation.
It should be working, this would have been a problem for a short time using galaxy-central, but should not have affected -dist. Could you send the output of:
python ./scripts/get_platforms.py python -V
Should I be running galaxy-central instead?
No, galaxy-dist is fine (and should be less prone to issues due to cloning/updating at the wrong moment).
Thanks, --nate
~Mike ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
-
Kanwei Li -
Michael Steder -
Nate Coraor