Re: [galaxy-dev] Installing tools with dependencies using mi-deployment scripts
Each use of fabric's `run` method is independent so they cannot be chained;
you would either need to prepend the export command to the command that
depends on the fact PYTHONPATH is set (e.g., run(export PYTHONPATH=...;
command that requires given PP) or (better approach) create an env.sh
file in the Qiime's install dir so that it includes the required 'export
PYTHONPATH=...'. When Galaxy invokes Qiime, it will automatically source
that env.sh (assuming you have config variable `tool_dependency_dir =
/mnt/galaxyTools/tools` set in Galaxy's universe_wsgi.ini).
Enis
On Fri, Jul 15, 2011 at 12:19 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello Enis,
I am trying to add PyCogent to the PYTHONPATH, but it seems the Fabric
run command does not recognize it.
I tried: run(export
PYTHONPATH=/mnt/galaxyTools/tools/PyCogent/1.5.1/lib/python2.6/site-packages/:$PYTHONPATH)
and then use cmd_install() to install Galaxy, but I keep getting the
message that PyCogent is not installed.
The normal strategy to use sys.path will not work because that will
adjust the PYTHONPATH on my local machine, not in the image if I am
correct.
Do you know a way to set the PYTHONPATH for Fabric' run() command?
Thanks,
Mattias
On Thu, 2011-07-14 at 09:05 +, Enis Afgan wrote:
Hi Mattias,
PyCogent is not currently being installed as part of mi-deployment, so
the method for installing it should be added (if you do so, please
consider issuing a pull request on bitbucket so it can be added to the
project).
When it comes to composing $PYTHONPATH to include the reference to
PyCogent via Qiime's env.sh - this should be done as part of the Qiime
installation method in mi-deployment (something like export
PYHTONPATH=path where PyCogent was installed; export PATH=...).
Sourcing of the tool's env.sh script is prepended to the execution
command when running the tool so the appropriate environment settings
will be loaded before the tool is run.
Enis
On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello,
I am trying to add tools (PyCogent, Qiime) to a Cloudman image
using the
mi-deployment scripts. Qiime depends on PyCogent and it needs
to be
accessible on the python path, otherwise I get an error:
PyCogent not installed but required. (Is it installed? Is it
in the
current user's $PYTHONPATH or site-packages?)
Is there a way to add the paths in env.sh to the sys.path
during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I only
receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]:
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
'/mnt/galaxyTools/tools/blast/2.2.25',
'2.2.25')
Is there a smarter way to add files to the PYTHONPATH during
the
execution of tools_fabfile.py?
Thanks,
Mattias
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
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Re: [galaxy-dev] Installing tools with dependencies using mi-deployment scripts
I just found out the former approach you mentioned. Its now installing
perfectly. The latter approach won't work for a Qiime installation
because its needs PyCogent on its path during the setup.py phase.
Thanks for clarification.
If I finished adding Qiime' dependencies I will put it on bitbucket.
Greetz,
Mattias
On Fri, 2011-07-15 at 13:44 +, Enis Afgan wrote:
Each use of fabric's `run` method is independent so they cannot be
chained; you would either need to prepend the export command to the
command that depends on the fact PYTHONPATH is set (e.g., run(export
PYTHONPATH=...; command that requires given PP) or (better
approach) create an env.sh file in the Qiime's install dir so that it
includes the required 'export PYTHONPATH=...'. When Galaxy invokes
Qiime, it will automatically source that env.sh (assuming you have
config variable `tool_dependency_dir = /mnt/galaxyTools/tools` set in
Galaxy's universe_wsgi.ini).
Enis
On Fri, Jul 15, 2011 at 12:19 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello Enis,
I am trying to add PyCogent to the PYTHONPATH, but it seems
the Fabric
run command does not recognize it.
I tried: run(export
PYTHONPATH=/mnt/galaxyTools/tools/PyCogent/1.5.1/lib/python2.6/site-packages/:$PYTHONPATH)
and then use cmd_install() to install Galaxy, but I keep
getting the
message that PyCogent is not installed.
The normal strategy to use sys.path will not work because that
will
adjust the PYTHONPATH on my local machine, not in the image if
I am
correct.
Do you know a way to set the PYTHONPATH for Fabric' run()
command?
Thanks,
Mattias
On Thu, 2011-07-14 at 09:05 +, Enis Afgan wrote:
Hi Mattias,
PyCogent is not currently being installed as part of
mi-deployment, so
the method for installing it should be added (if you do so,
please
consider issuing a pull request on bitbucket so it can be
added to the
project).
When it comes to composing $PYTHONPATH to include the
reference to
PyCogent via Qiime's env.sh - this should be done as part of
the Qiime
installation method in mi-deployment (something like export
PYHTONPATH=path where PyCogent was installed; export
PATH=...).
Sourcing of the tool's env.sh script is prepended to the
execution
command when running the tool so the appropriate environment
settings
will be loaded before the tool is run.
Enis
On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello,
I am trying to add tools (PyCogent, Qiime) to a
Cloudman image
using the
mi-deployment scripts. Qiime depends on PyCogent and
it needs
to be
accessible on the python path, otherwise I get an
error:
PyCogent not installed but required. (Is it
installed? Is it
in the
current user's $PYTHONPATH or site-packages?)
Is there a way to add the paths in env.sh to the
sys.path
during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I
only
receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]:
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
'/mnt/galaxyTools/tools/blast/2.2.25',
'2.2.25')
Is there a smarter way to add files to the
PYTHONPATH during
the
execution of tools_fabfile.py?
Thanks,
Mattias
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Re: [galaxy-dev] Installing tools with dependencies using mi-deployment scripts
Hi Mattias,
PyCogent is not currently being installed as part of mi-deployment, so the
method for installing it should be added (if you do so, please consider
issuing a pull request on bitbucket so it can be added to the project).
When it comes to composing $PYTHONPATH to include the reference to PyCogent
via Qiime's env.sh - this should be done as part of the Qiime installation
method in mi-deployment (something like export PYHTONPATH=path where
PyCogent was installed; export PATH=...).
Sourcing of the tool's env.sh script is prepended to the execution command
when running the tool so the appropriate environment settings will be loaded
before the tool is run.
Enis
On Wed, Jul 13, 2011 at 12:09 PM, Mattias de Hollander
m.dehollan...@nioo.knaw.nl wrote:
Hello,
I am trying to add tools (PyCogent, Qiime) to a Cloudman image using the
mi-deployment scripts. Qiime depends on PyCogent and it needs to be
accessible on the python path, otherwise I get an error:
PyCogent not installed but required. (Is it installed? Is it in the
current user's $PYTHONPATH or site-packages?)
Is there a way to add the paths in env.sh to the sys.path during
installation using tools_fabfile.py?
All the tools are in /mnt/galaxyTools/tools.
I tried the DependencyManager from galaxy but then I only receive the
path to the env.sh file:
In [43]: dependency_manager.find_dep('blast')
Out[43]:
('/mnt/galaxyTools/tools/blast/2.2.25/env.sh',
'/mnt/galaxyTools/tools/blast/2.2.25',
'2.2.25')
Is there a smarter way to add files to the PYTHONPATH during the
execution of tools_fabfile.py?
Thanks,
Mattias
--
Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
___
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:
http://lists.bx.psu.edu/
