Oren,
I've moved this thread over to the galaxy-dev mailing list since it deals with a local installation. Users on this list are more likely to have an answer for this type of question.
That said, we don't officially support running Galaxy under Cygwin (or Windows at all), and I don't know of anyone running such an instance. If you *do* manage to get things working on Windows, however, it'd certainly be useful to know what you had to go through to make it happen. One relatively painless option for running galaxy under windows, and what I'd suggest, would be to use the virtual machine we provide at usegalaxy.org/vm.
Let me know if you have any other questions, and good luck!
-Dannon
On Oct 12, 2011, at 02:50 PM, Oren Livne livne@uchicago.edu wrote:
Dear All,
There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error?
This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front.
Thank you so much, Oren
-------- $ python --version Python 2.6.5
oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg 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-01-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py26.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/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 Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
___________________________________________________________ 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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Dannon Baker wrote:
Oren,
I've moved this thread over to the galaxy-dev mailing list since it deals with a local installation. Users on this list are more likely to have an answer for this type of question.
That said, we don't officially support running Galaxy under Cygwin (or Windows at all), and I don't know of anyone running such an instance. If you *do* manage to get things working on Windows, however, it'd certainly be useful to know what you had to go through to make it happen. One relatively painless option for running galaxy under windows, and what I'd suggest, would be to use the virtual machine we provide at usegalaxy.org/vm.
Let me know if you have any other questions, and good luck!
-Dannon
Oren,
In addition to everything Dannon said, I'll add that the specific problem here is that we don't pre-build Python eggs for Cygwin. If you're still trying to do this, I'd suggest running scripts/fetch_eggs.py once to grab all platform-agnostic eggs, and then scripts/scramble.py to try to build the rest. Good luck!
--nate
On Oct 12, 2011, at 02:50 PM, Oren Livne livne@uchicago.edu wrote:
Dear All,
There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error?
This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front.
Thank you so much, Oren
$ python --version Python 2.6.5
oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg 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-01-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py26.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/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 Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
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:
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:
Dear Nate,
I've been doing exactly that. What's driving me crazy is that every second compile (bx_python, numpy, pysam) runs into a Cygwin DLL remap failure that cannot be resolved with /bin/rebaseall. So any advice on how to get rid of that would be great. Right now it's failing in the bx_python build on lapack_lite.dll or mtrand.dll (or randomly on a bunch of other cyg* dlls).
Thanks, Oren
Oren,
In addition to everything Dannon said, I'll add that the specific problem here is that we don't pre-build Python eggs for Cygwin. If you're still trying to do this, I'd suggest running scripts/fetch_eggs.py once to grab all platform-agnostic eggs, and then scripts/scramble.py to try to build the rest. Good luck!
--nate
On Oct 12, 2011, at 02:50 PM, Oren Livnelivne@uchicago.edu wrote:
Dear All,
There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error?
This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front.
Thank you so much, Oren
$ python --version Python 2.6.5
oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg 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-01-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py26.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/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 Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in<module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
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:
http://lists.bx.psu.edu/ ___________________________________________________________ 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:
Oren Livne wrote:
Dear Nate,
I've been doing exactly that. What's driving me crazy is that every second compile (bx_python, numpy, pysam) runs into a Cygwin DLL remap failure that cannot be resolved with /bin/rebaseall. So any advice on how to get rid of that would be great. Right now it's failing in the bx_python build on lapack_lite.dll or mtrand.dll (or randomly on a bunch of other cyg* dlls).
Hi Oren,
I've used Cygwin once, so I'm afraid I can't be of any help here.
--nate
Thanks, Oren
Oren,
In addition to everything Dannon said, I'll add that the specific problem here is that we don't pre-build Python eggs for Cygwin. If you're still trying to do this, I'd suggest running scripts/fetch_eggs.py once to grab all platform-agnostic eggs, and then scripts/scramble.py to try to build the rest. Good luck!
--nate
On Oct 12, 2011, at 02:50 PM, Oren Livnelivne@uchicago.edu wrote:
Dear All,
There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error?
This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front.
Thank you so much, Oren
$ python --version Python 2.6.5
oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg 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-01-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py26.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/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 Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in<module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.
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:
http://lists.bx.psu.edu/ ___________________________________________________________ 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:
galaxy-dev@lists.galaxyproject.org
-
Dannon Baker -
Nate Coraor -
Oren Livne