Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were: - create a virtualenv environment and activate it - get galaxy-dist and call run.sh - it asked me to build quite a lot of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems. - shut down galaxy-dist, and in another directory, get galaxy-central and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
On 1 August 2012 15:28, Clare Sloggett sloc@unimelb.edu.au wrote:
I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist.
oops, of course I mean 'so want to run galaxy-central.'
Clare-
Have you resolved this yet? I had seen similar issues with respect to pycrypto before I used virtualenv, but I don't believe that I saw it afterwards. I'll take a look and see if I can reproduce it.
I only have obvious things to recommend right now. For example, make sure that the environment has been loaded each time. Check http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server#Use_a... , which I'm sure you've already done.
-Scott
----- Original Message -----
On 1 August 2012 15:28, Clare Sloggett sloc@unimelb.edu.au wrote:
I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist.
oops, of course I mean 'so want to run galaxy-central.'
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
Hi Scott,
Thanks very much for this!
virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: .....
which is where I set up my environment.
I'm not using anything in particular outside Enthought, that I can think of. Enthought packages up a whole lot of things including scipy.
The strange thing is that galaxy-dist runs but galaxy-central doesn't. So, I was hoping it would actually be a temporary bug in the egg distribution, but it sounds like the problem really is my environment. I don't understand how Enthought can be causing problems that virtualenv can't work around, but I've never really understood how python is structured in OSX! So I think it's probably worth me going through the effort of setting up a working environment in an ubuntu VM rather than running it on my Mac - I don't want to be asking you to pull code changes from an environment that's unusual.
I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). So far I've pulled the code into the vm and run it, without virtualenv, and it gives none of the errors I see on the Mac. My plan is to both share the drive containing galaxy-central and share the network so that I can do both the editing and the browsing on my host machine, but if there are better ways advice is welcome!
Thanks, Clare
On 2 August 2012 07:26, Scott McManus scottmcmanus@gatech.edu wrote:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
Hi Clare,
I ran into the same problem as well when I upgraded my galaxy-central version. I am running Mac Os10.6.8
What I did to get use the command *$ pip install fabric*
It manually fetches the latest version of fabric from pip ( http://www.pip-installer.org/en/latest/index.html) which is a package manager from python, also its dependencies:* ssh* and *pycrypto,* which are the components causing the problem. I think it might be due to an erroneous version of the egg hosted on galaxy.
Works fine after that for me.
Cheers Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett sloc@unimelb.edu.auwrote:
Hi Scott,
Thanks very much for this!
virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: .....
which is where I set up my environment.
I'm not using anything in particular outside Enthought, that I can think of. Enthought packages up a whole lot of things including scipy.
The strange thing is that galaxy-dist runs but galaxy-central doesn't. So, I was hoping it would actually be a temporary bug in the egg distribution, but it sounds like the problem really is my environment. I don't understand how Enthought can be causing problems that virtualenv can't work around, but I've never really understood how python is structured in OSX! So I think it's probably worth me going through the effort of setting up a working environment in an ubuntu VM rather than running it on my Mac - I don't want to be asking you to pull code changes from an environment that's unusual.
I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). So far I've pulled the code into the vm and run it, without virtualenv, and it gives none of the errors I see on the Mac. My plan is to both share the drive containing galaxy-central and share the network so that I can do both the editing and the browsing on my host machine, but if there are better ways advice is welcome!
Thanks, Clare
On 2 August 2012 07:26, Scott McManus scottmcmanus@gatech.edu wrote:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File
"/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
Hi Tomithy,
Thanks, this worked for me too!
Just to be clear for interested devs:
If I run galaxy-dist on my mac it asks me to build a whole series of eggs by hand using scripts/scramble.py, and if I follow these instructions, galaxy runs. A bit tedious but trivial to do.
If I run galaxy-central on my mac the same thing happens for a few dependencies, but then it gets stuck at the error I posted originally. If I run `pip install fabric` as Tomithy suggests then I get the same results as running galaxy-dist, ie galaxy works after using scramble.py a few times.
If I run galaxy-central (or presumably galaxy-dist) on ubuntu it doesn't complain about any of the dependencies, doesn't get stuck, and doesn't ask me to build any eggs by hand.
So I'm now wondering if, for code editing, I should use the ubuntu environment I've set up even though the code is working natively on the mac, just to avoid future complications.
Cheers, Clare
On 19 August 2012 21:36, Tomithy Too tomithy.too@gmail.com wrote:
Hi Clare,
I ran into the same problem as well when I upgraded my galaxy-central version. I am running Mac Os10.6.8
What I did to get use the command $ pip install fabric
It manually fetches the latest version of fabric from pip (http://www.pip-installer.org/en/latest/index.html) which is a package manager from python, also its dependencies: ssh and pycrypto, which are the components causing the problem. I think it might be due to an erroneous version of the egg hosted on galaxy.
Works fine after that for me.
Cheers Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett sloc@unimelb.edu.au wrote:
Hi Scott,
Thanks very much for this!
virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: .....
which is where I set up my environment.
I'm not using anything in particular outside Enthought, that I can think of. Enthought packages up a whole lot of things including scipy.
The strange thing is that galaxy-dist runs but galaxy-central doesn't. So, I was hoping it would actually be a temporary bug in the egg distribution, but it sounds like the problem really is my environment. I don't understand how Enthought can be causing problems that virtualenv can't work around, but I've never really understood how python is structured in OSX! So I think it's probably worth me going through the effort of setting up a working environment in an ubuntu VM rather than running it on my Mac - I don't want to be asking you to pull code changes from an environment that's unusual.
I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). So far I've pulled the code into the vm and run it, without virtualenv, and it gives none of the errors I see on the Mac. My plan is to both share the drive containing galaxy-central and share the network so that I can do both the editing and the browsing on my host machine, but if there are better ways advice is welcome!
Thanks, Clare
On 2 August 2012 07:26, Scott McManus scottmcmanus@gatech.edu wrote:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File
"/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
Hi Clare,
If you use the system python, or a build from python.org, you should be fine. It's Enthought python, which is only built for a single architecture, that's the reason for having to do so much manual egg building.
--nate
On Aug 19, 2012, at 7:36 AM, Tomithy Too wrote:
Hi Clare,
I ran into the same problem as well when I upgraded my galaxy-central version. I am running Mac Os10.6.8
What I did to get use the command $ pip install fabric
It manually fetches the latest version of fabric from pip (http://www.pip-installer.org/en/latest/index.html) which is a package manager from python, also its dependencies: ssh and pycrypto, which are the components causing the problem. I think it might be due to an erroneous version of the egg hosted on galaxy.
Works fine after that for me.
Cheers Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett sloc@unimelb.edu.au wrote: Hi Scott,
Thanks very much for this!
virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: .....
which is where I set up my environment.
I'm not using anything in particular outside Enthought, that I can think of. Enthought packages up a whole lot of things including scipy.
The strange thing is that galaxy-dist runs but galaxy-central doesn't. So, I was hoping it would actually be a temporary bug in the egg distribution, but it sounds like the problem really is my environment. I don't understand how Enthought can be causing problems that virtualenv can't work around, but I've never really understood how python is structured in OSX! So I think it's probably worth me going through the effort of setting up a working environment in an ubuntu VM rather than running it on my Mac - I don't want to be asking you to pull code changes from an environment that's unusual.
I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). So far I've pulled the code into the vm and run it, without virtualenv, and it gives none of the errors I see on the Mac. My plan is to both share the drive containing galaxy-central and share the network so that I can do both the editing and the browsing on my host machine, but if there are better ways advice is welcome!
Thanks, Clare
On 2 August 2012 07:26, Scott McManus scottmcmanus@gatech.edu wrote:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
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Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
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Hi Nate & all,
I see - enthought changes the default python version, and virtualenv was giving me a python version based on the version I used to run virtualenv. If I run /usr/bin/python virtualenv.py galaxy_central_syspython . galaxy_central_syspython/bin/activate
and then pull galaxy-central and run it, I don't get any egg errors, either the build-by-hand ones or the more serious error that stopped me originally.
Thanks!
Clare
On 22 August 2012 01:26, Nate Coraor nate@bx.psu.edu wrote:
Hi Clare,
If you use the system python, or a build from python.org, you should be fine. It's Enthought python, which is only built for a single architecture, that's the reason for having to do so much manual egg building.
--nate
On Aug 19, 2012, at 7:36 AM, Tomithy Too wrote:
Hi Clare,
I ran into the same problem as well when I upgraded my galaxy-central version. I am running Mac Os10.6.8
What I did to get use the command $ pip install fabric
It manually fetches the latest version of fabric from pip (http://www.pip-installer.org/en/latest/index.html) which is a package manager from python, also its dependencies: ssh and pycrypto, which are the components causing the problem. I think it might be due to an erroneous version of the egg hosted on galaxy.
Works fine after that for me.
Cheers Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett sloc@unimelb.edu.au wrote: Hi Scott,
Thanks very much for this!
virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: .....
which is where I set up my environment.
I'm not using anything in particular outside Enthought, that I can think of. Enthought packages up a whole lot of things including scipy.
The strange thing is that galaxy-dist runs but galaxy-central doesn't. So, I was hoping it would actually be a temporary bug in the egg distribution, but it sounds like the problem really is my environment. I don't understand how Enthought can be causing problems that virtualenv can't work around, but I've never really understood how python is structured in OSX! So I think it's probably worth me going through the effort of setting up a working environment in an ubuntu VM rather than running it on my Mac - I don't want to be asking you to pull code changes from an environment that's unusual.
I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1). So far I've pulled the code into the vm and run it, without virtualenv, and it gives none of the errors I see on the Mac. My plan is to both share the drive containing galaxy-central and share the network so that I can do both the editing and the browsing on my host machine, but if there are better ways advice is welcome!
Thanks, Clare
On 2 August 2012 07:26, Scott McManus scottmcmanus@gatech.edu wrote:
I haven't been able to reproduce this yet with the instructions you gave, but I'm not using the same environment. Can you give me an idea of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being sourced correctly. We can check if it's actually using the correct environment by calling "echo $PATH" and checking that the path is pointing to the virtual environment. For example, I installed virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and I got: (galaxy_env)$ echo $PATH /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
-Scott
----- Original Message -----
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around with some changes, and I'm having trouble getting it to run. I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. I'm not trying to install any extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought installed, and I assume I will be using its version of python by default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and galaxy-central (though it doesn't seem to matter if I give galaxy-central its own environment, I see the same error). So the steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh --reload Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: pycrypto (a dependent egg of Fabric) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "ssh" requires "pycrypto>=2.1,!=2.4" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto>=2.1,!=2.4')) Fetch failed.
Any idea what is causing this?
Thanks, Clare
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
--
Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___________________________________________________________ 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:
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
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Clare Sloggett -
Nate Coraor -
Scott McManus -
Tomithy Too