[galaxy-dev] Error starting Galaxy after update of March 2012
Hi,
I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm
now unable to start Galaxy..
Here is the content of Galaxy_log:
Traceback (most recent call last):
File "/galaxy-dist/lib/galaxy/web/buildapp.py", line 81,
in app_factory
from galaxy.app import UniverseApplication
File "/galaxy-dist/lib/galaxy/app.py", line 11, in
from galaxy.objectstore import build_object_store_from_config
File "/galaxy-dist/lib/galaxy/objectstore/__init__.py",
line 27, in
from galaxy.objectstore.s3_multipart_upload import multipart_upload
File
"/galaxy-dist/lib/galaxy/objectstore/s3_multipart_upload.py",
line 22, in
eggs.require('boto')
File "/galaxy-dist/lib/galaxy/eggs/__init__.py", line 415,
in require
raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
EggNotFetchable: ['boto']
Removing PID file /galaxy-dist/galaxy.pid
Is that an error specific to our instance?
Is there a way to downgrade Galaxy?
Thanks by advance for your answer..
Alban
--
Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
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Re: [galaxy-dev] Error starting Galaxy after update of March 2012
Nate Coraor wrote:
> On Mar 13, 2012, at 10:36 AM, Alban Lermine wrote:
>
>
>> Hi,
>>
>> I run upgrade: hg pull -u -r 40f1816d6857 on our local instance, and I'm
>> now unable to start Galaxy..
>>
>> Here is the content of Galaxy_log:
>>
>> Traceback (most recent call last):
>> File "/galaxy-dist/lib/galaxy/web/buildapp.py", line 81,
>> in app_factory
>>from galaxy.app import UniverseApplication
>> File "/galaxy-dist/lib/galaxy/app.py", line 11, in
>>from galaxy.objectstore import build_object_store_from_config
>> File "/galaxy-dist/lib/galaxy/objectstore/__init__.py",
>> line 27, in
>>from galaxy.objectstore.s3_multipart_upload import multipart_upload
>> File
>> "/galaxy-dist/lib/galaxy/objectstore/s3_multipart_upload.py",
>> line 22, in
>>eggs.require('boto')
>> File "/galaxy-dist/lib/galaxy/eggs/__init__.py", line 415,
>> in require
>>raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
>> EggNotFetchable: ['boto']
>> Removing PID file /galaxy-dist/galaxy.pid
>>
>> Is that an error specific to our instance?
>>
>
> Hi Alban,
>
> Is your Galaxy server behind a firewall or without network access such that
> it cannot access http://eggs.g2.bx.psu.edu/ ?
>
> What happens if you run `python scripts/fetch_eggs.py` by hand?
>
>
>> Is there a way to downgrade Galaxy?
>>
>
> Yes, in most cases you can downgrade with `hg update -r `.
>
> --nate
>
>
>
>
>> Thanks by advance for your answer..
>>
>> Alban
>>
>>
>> --
>> Alban Lermine
>> Unité 900 : Inserm - Mines ParisTech - Institut Curie
>> « Bioinformatics and Computational Systems Biology of Cancer »
>> 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
>> Tel : +33 (0) 1 56 24 69 84
>>
>> ___
>> 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/
>>
>>
>
>
Re,
Thanks for your fast answer..
I run fetch_eggs.py by hand, here is the return:
Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg
Removed conflicting egg: /galaxy-dist/eggs/boto-1.8d-py2.6.egg
I tried then to start Galaxy, and I also have a new error message:
Traceback (most recent call last):
File
"/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py",
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File
"/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py",
line 24, in __init__
self.config.check()
File
"/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py",
line 254, in check
raise ConfigurationError( "Unable to create missing directory:
%s\n%s" % ( path, e ) )
ConfigurationError: Unable to create missing directory: ./../shed_tools
[Errno 13] Permission denied: './../shed_tools'
It seems it's now only a permission problem.. (I only have rights on
galaxy-dist directory), I will ask our system engineer to rerun update..
Alban
--
Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
___
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/
Re: [galaxy-dev] Error starting Galaxy after update of March 2012
Nate Coraor wrote: > On Mar 13, 2012, at 11:08 AM, Alban Lermine wrote: > > >>> Hi Alban, >>> >>> Is your Galaxy server behind a firewall or without network access such that >>> it cannot access http://eggs.g2.bx.psu.edu/ ? >>> >>> What happens if you run `python scripts/fetch_eggs.py` by hand? >>> >>> >>> >>>> Is there a way to downgrade Galaxy? >>>> >>>> >>> Yes, in most cases you can downgrade with `hg update -r `. >>> >>> --nate >>> >>> >>> >>> >>> >>>> Thanks by advance for your answer.. >>>> >>>> Alban >>>> >>>> >>>> -- >>>> Alban Lermine >>>> Unité 900 : Inserm - Mines ParisTech - Institut Curie >>>> « Bioinformatics and Computational Systems Biology of Cancer » >>>> 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France >>>> Tel : +33 (0) 1 56 24 69 84 >>>> >>>> ___ >>>> 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/ >>>> >>>> >>>> >>> >> Re, >> >> Thanks for your fast answer.. >> >> I run fetch_eggs.py by hand, here is the return: >> >> Fetched http://eggs.g2.bx.psu.edu/boto/boto-2.2.2-py2.6.egg >> Removed conflicting egg: /galaxy-dist/eggs/boto-1.8d-py2.6.egg >> >> I tried then to start Galaxy, and I also have a new error message: >> >> Traceback (most recent call last): >> File >> "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/web/buildapp.py", >> line 82, in app_factory >>app = UniverseApplication( global_conf = global_conf, **kwargs ) >> File >> "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/app.py", >> line 24, in __init__ >>self.config.check() >> File >> "/bioinfo/http/prod/hosted/galaxy.curie.fr/galaxy-dist/lib/galaxy/config.py", >> line 254, in check >>raise ConfigurationError( "Unable to create missing directory: >> %s\n%s" % ( path, e ) ) >> ConfigurationError: Unable to create missing directory: ./../shed_tools >> [Errno 13] Permission denied: './../shed_tools' >> >> It seems it's now only a permission problem.. (I only have rights on >> galaxy-dist directory), I will ask our system engineer to rerun update.. >> > > Hi Alban, > > You can fix this one by changing the path to the shed_tools directory in > shed_tool_conf.xml. It can be any directory you can write to, but should not > be underneath the galaxy-dist directory. > > --nate > > >> Alban >> >> -- >> Alban Lermine >> Unité 900 : Inserm - Mines ParisTech - Institut Curie >> « Bioinformatics and Computational Systems Biology of Cancer » >> 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France >> Tel : +33 (0) 1 56 24 69 84 >> >> > > It's working again, great thanks, Alban -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
[galaxy-dev] Same error in multiple tools
Hi, I have the same error message for multiple tools (GFFtoBED, BEDtoBIGBED,BAMtoSAM,...): /from galaxy import eggs ImportError: No module named galaxy It's happening only since the last upgrade, do you know what is going wrong? Thanks, Alban / -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] Same error in multiple tools
Hi, I'm running these tools on a cluster.. Alban Emil Bouvier wrote: > Alban, > > Are you running these tools on a cluster, or on a local system? > >Dave B. > > On 3/19/12 6:55 AM, Alban Lermine wrote: >> Hi, >> >> I have the same error message for multiple tools (GFFtoBED, >> BEDtoBIGBED,BAMtoSAM,...): >> >> /from galaxy import eggs >> ImportError: No module named galaxy >> >> It's happening only since the last upgrade, do you know what is going >> wrong? >> >> Thanks, >> >> Alban >> / >> -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] Same error in multiple tools
Hi, It seems that PYTHONPATH isn't set when galaxy start.. (according to http://osdir.com/ml/galaxy-development-source-control/2011-11/msg00035.html) Should I search this way ? Thanks by advance, Alban Alban Lermine wrote: > Hi, > > I'm running these tools on a cluster.. > > > Alban > > Emil Bouvier wrote: > >> Alban, >> >> Are you running these tools on a cluster, or on a local system? >> >>Dave B. >> >> On 3/19/12 6:55 AM, Alban Lermine wrote: >> >>> Hi, >>> >>> I have the same error message for multiple tools (GFFtoBED, >>> BEDtoBIGBED,BAMtoSAM,...): >>> >>> /from galaxy import eggs >>> ImportError: No module named galaxy >>> >>> It's happening only since the last upgrade, do you know what is going >>> wrong? >>> >>> Thanks, >>> >>> Alban >>> / >>> >>> > > > -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] Error: Job output not returned from cluster
rstrip("\n")
#Original job launcher
#job_id = pbs.pbs_submit(c, job_attrs, job_file, pbs_queue_name, None)
pbs.pbs_disconnect(c)
Second thing I have done is to wait error and output file from torque in
the finish_job function (if not, I never receive the output, seems to be
your problem..), here is the code used:
def finish_job( self, pbs_job_state ):
"""
Get the output/error for a finished job, pass to
`job_wrapper.finish`
and cleanup all the PBS temporary files.
"""
ofile = pbs_job_state.ofile
efile = pbs_job_state.efile
job_file = pbs_job_state.job_file
# collect the output
try:
# With qsub system call, need to wait efile and ofile creation
at the end of the job execution before reading them
efileExists = os.path.isfile(efile)
ofileExists = os.path.isfile(ofile)
efileExistsSTR = str(efileExists)
ofileExistsSTR = str(ofileExists)
while efileExistsSTR == "False":
time.sleep( 1 )
efileExists = os.path.isfile(efile)
efileExistsSTR = str(efileExists)
while ofileExistsSTR == "False":
time.sleep( 1 )
ofileExists = os.path.isfile(ofile)
ofileExistsSTR = str(ofileExists)
# Back to original code
ofh = file(ofile, "r")
efh = file(efile, "r")
stdout = ofh.read( 32768 )
stderr = efh.read( 32768 )
except:
stdout = ''
stderr = 'Job output not returned by PBS: the output
datasets were deleted while the job was running, the job was manually
dequeued or there was a cluster error.'
log.debug(stderr)
* Last step is to allow galaxy user to run sudo
Hope it can help you finding your problem..
See you,
Alban
--
Alban Lermine
Unité 900 : Inserm - Mines ParisTech - Institut Curie
« Bioinformatics and Computational Systems Biology of Cancer »
11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France
Tel : +33 (0) 1 56 24 69 84
___
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/
Re: [galaxy-dev] Sharing data in Cistrome
Hi, Did you have special characters (é, à,...) in the email of the person you try to share with? If so, try whitout this special characters (è -> e or à -> a), it should works.. Bests, Alban Le 07/06/2012 16:26, Päivi Pihlajamaa a écrit : > Hi, > > I am trying to share my files/history in Galaxy/Cistrome with my > colleague, but the 'Share with user' link gives the following error. > Could you please help me, am i doing something wrong or is there a bug > in the system? > > Best regards, > Päivi > > Server Error > URL: > http://cistrome.org/ap/history/share?use_panels=False&id=7b2014ae6b4b7c3f > Module paste.exceptions.errormiddleware:143 in __call__ >>> app_iter = self.application(environ, start_response) > Module paste.debug.prints:98 in __call__ >>> environ, self.app) > Module paste.wsgilib:539 in intercept_output >>> app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ >>> return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ >>> return self.application(environ, start_response) > Module galaxy.web.framework.base:160 in __call__ >>> body = method( trans, **kwargs ) > Module galaxy.web.framework:90 in decorator >>> return func( self, trans, *args, **kwargs ) > Module galaxy.web.controllers.history:960 in share >>> send_to_err=send_to_err ) > Module galaxy.web.framework:733 in fill_template >>> return self.fill_template_mako( filename, **kwargs ) > Module galaxy.web.framework:744 in fill_template_mako >>> return template.render( **data ) > Module mako.template:296 in render >>> return runtime._render(self, self.callable_, args, data) > Module mako.runtime:660 in _render >>> **_kwargs_for_callable(callable_, data)) > Module mako.runtime:692 in _render_context >>> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) > Module mako.runtime:718 in _exec_template >>> callable_(context, *args, **kwargs) > Module _base_mako:42 in render_body >>> __M_writer(unicode(next.body())) > Module _history_share_mako:74 in render_body >>> __M_writer(unicode(history.name)) > UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position > 1: ordinal not in range(128) -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] How to upload local files in Galaxy
Hi, There is also another solution if you don't want let users being able to create libraries. We have implemented this solution in our local production server here at Institut Curie. We add a tool call "local upload file", that takes as entry parameters the name of the dataset, the type of file and the path to the file you want to upload. At the execution, the bash script behind will remove the output dataset created by Galaxy and replaced it by a symbolic link to the file (so you don't duplicate files). Just to warn you, there could be a security failure with this tool, because if it is locally executed, it will be by the Galaxy applicative user that can potentially have more rights on file than the current user. To go through this failure, we execute this tool on our local cluster (with pbs/torque) as the current user (so if the current user try to upload a file that he doesn't owned, the tool will not be able to create the symbolic link and the user will receive an error on the Galaxy interface). Tell me if you're interested in such a tool, and I send you the xml file and bash script associated. Bests, Alban Le 07/06/2012 20:11, Mehmet Belgin a écrit : > Brad, > > Thank you for your fast reply! Looks like "library_import_dir" is for > admins and there is another library option for users. I will try with > that one and see if the files appear in the GUI. > > Thanks! > > > = > Mehmet Belgin, Ph.D. (mehmet.bel...@oit.gatech.edu > <mailto:mehmet.bel...@oit.gatech.edu>) > Scientific Computing Consultant | OIT - Academic and Research Technologies > Georgia Institute of Technology > 258 Fourth Street, Rich Building, Room 326 > Atlanta, GA 30332-0700 > Office: (404) 385-0665 > > > > > On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote: > >> Mehmet: >> >> It's not important how the files get there, they could be moved via >> ftp, scp, cp, smb - whatever. >> Galaxy will use that directory to import from no matter how the files >> arrive. >> >> I found that confusing at first too. >> >> Brad >> On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: >> >>> Hi Everyone, >>> >>> I am helping a research group to use Galaxy on our clusters. >>> Unfortunately I have no previous experience with Galaxy, but >>> learning along the way. We are almost there, but cannot figure out >>> one particular issue. This is about configuration of Galaxy, so I >>> thought developers list is a better place to submit than the user list. >>> >>> The galaxy web interface allows for either copy/paste of text, or a >>> URL. Unfortunately we cannot setup a FTP server as instructed due to >>> restrictions on the cluster. The files we are trying to upload are >>> large; around 2GB in size. It does not make sense to upload these >>> files to a remote location (which we can provide an URL for) and >>> download them back, since the data and galaxy are on the same >>> system. However, I could not find a way to open these files locally. >>> >>> I did some reading, and hoped that "library_import_dir" in >>> "universe_wsgi.ini" would do the trick, but it didn't. Therefore, I >>> will really appreciate any suggestions. >>> >>> Thanks a lot in advance! >>> >>> -Mehmet >>> >>> >>> >>> >>> >>> ___ >>> 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/ >> >> -- >> Brad Langhorst >> langho...@neb.com <mailto:langho...@neb.com> >> 978-380-7564 >> >> >> >> > > > ___ > 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/ -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84 ___ 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/
Re: [galaxy-dev] How to upload local files in Galaxy
Hi all, Despite the possible security failure, I push the upload_local_tool in main toolshed under the "data source" repository. I notice about the possible security failure and the way to fix it. I also have a simple 5 minutes method to modify existing tools to allow users to choose the directory where to write the outputs (to keep working with your own tree whitout breaking Galaxy database links). Tell me if you are interested in this method.. Bests, Alban > Hello, > > I am interested in this "local upload file" tool. Can you please send > the files to me as well. > > Thanks. > -Raj > > On 6/8/12 4:36 AM, Alban Lermine wrote: >> Hi, >> >> There is also another solution if you don't want let users being able >> to create libraries. >> We have implemented this solution in our local production server here >> at Institut Curie. >> We add a tool call "local upload file", that takes as entry >> parameters the name of the dataset, the type of file and the path to >> the file you want to upload. >> At the execution, the bash script behind will remove the output >> dataset created by Galaxy and replaced it by a symbolic link to the >> file (so you don't duplicate files). >> Just to warn you, there could be a security failure with this tool, >> because if it is locally executed, it will be by the Galaxy >> applicative user that can potentially have more rights on file than >> the current user. >> To go through this failure, we execute this tool on our local cluster >> (with pbs/torque) as the current user (so if the current user try to >> upload a file that he doesn't owned, the tool will not be able to >> create the symbolic link and the user will receive an error on the >> Galaxy interface). >> >> Tell me if you're interested in such a tool, and I send you the xml >> file and bash script associated. >> >> Bests, >> >> Alban >> >> >> >> Le 07/06/2012 20:11, Mehmet Belgin a écrit : >>> Brad, >>> >>> Thank you for your fast reply! Looks like "library_import_dir" is >>> for admins and there is another library option for users. I will try >>> with that one and see if the files appear in the GUI. >>> >>> Thanks! >>> >>> >>> = >>> Mehmet Belgin, Ph.D. (mehmet.bel...@oit.gatech.edu >>> <mailto:mehmet.bel...@oit.gatech.edu>) >>> Scientific Computing Consultant | OIT - Academic and Research >>> Technologies >>> Georgia Institute of Technology >>> 258 Fourth Street, Rich Building, Room 326 >>> Atlanta, GA 30332-0700 >>> Office: (404) 385-0665 >>> >>> >>> >>> >>> On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote: >>> >>>> Mehmet: >>>> >>>> It's not important how the files get there, they could be moved via >>>> ftp, scp, cp, smb - whatever. >>>> Galaxy will use that directory to import from no matter how the >>>> files arrive. >>>> >>>> I found that confusing at first too. >>>> >>>> Brad >>>> On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: >>>> >>>>> Hi Everyone, >>>>> >>>>> I am helping a research group to use Galaxy on our clusters. >>>>> Unfortunately I have no previous experience with Galaxy, but >>>>> learning along the way. We are almost there, but cannot figure out >>>>> one particular issue. This is about configuration of Galaxy, so I >>>>> thought developers list is a better place to submit than the user >>>>> list. >>>>> >>>>> The galaxy web interface allows for either copy/paste of text, or >>>>> a URL. Unfortunately we cannot setup a FTP server as instructed >>>>> due to restrictions on the cluster. The files we are trying to >>>>> upload are large; around 2GB in size. It does not make sense to >>>>> upload these files to a remote location (which we can provide an >>>>> URL for) and download them back, since the data and galaxy are on >>>>> the same system. However, I could not find a way to open these >>>>> files locally. >>>>> >>>>> I did some reading, and hoped that "library_import_dir" in >>>>> "universe_wsgi.ini" would do the trick, but it didn't. Therefore, >>>>> I will really a
Re: [galaxy-dev] How to upload local files in Galaxy
Re, My bad: upload_local_tool -> upload_local_file tool Bests, Alban > Hi all, > > Despite the possible security failure, I push the upload_local_tool in > main toolshed under the "data source" repository. > > I notice about the possible security failure and the way to fix it. > > I also have a simple 5 minutes method to modify existing tools to > allow users to choose the directory where to write the outputs (to > keep working with your own tree whitout breaking Galaxy database > links). Tell me if you are interested in this method.. Bests, > > Alban > > > >> Hello, >> >> I am interested in this "local upload file" tool. Can you please send >> the files to me as well. >> >> Thanks. >> -Raj >> >> On 6/8/12 4:36 AM, Alban Lermine wrote: >>> Hi, >>> >>> There is also another solution if you don't want let users being >>> able to create libraries. >>> We have implemented this solution in our local production server >>> here at Institut Curie. >>> We add a tool call "local upload file", that takes as entry >>> parameters the name of the dataset, the type of file and the path to >>> the file you want to upload. >>> At the execution, the bash script behind will remove the output >>> dataset created by Galaxy and replaced it by a symbolic link to the >>> file (so you don't duplicate files). >>> Just to warn you, there could be a security failure with this tool, >>> because if it is locally executed, it will be by the Galaxy >>> applicative user that can potentially have more rights on file than >>> the current user. >>> To go through this failure, we execute this tool on our local >>> cluster (with pbs/torque) as the current user (so if the current >>> user try to upload a file that he doesn't owned, the tool will not >>> be able to create the symbolic link and the user will receive an >>> error on the Galaxy interface). >>> >>> Tell me if you're interested in such a tool, and I send you the xml >>> file and bash script associated. >>> >>> Bests, >>> >>> Alban >>> >>> >>> >>> Le 07/06/2012 20:11, Mehmet Belgin a écrit : >>>> Brad, >>>> >>>> Thank you for your fast reply! Looks like "library_import_dir" is >>>> for admins and there is another library option for users. I will >>>> try with that one and see if the files appear in the GUI. >>>> >>>> Thanks! >>>> >>>> >>>> = >>>> Mehmet Belgin, Ph.D. (mehmet.bel...@oit.gatech.edu >>>> <mailto:mehmet.bel...@oit.gatech.edu>) >>>> Scientific Computing Consultant | OIT - Academic and Research >>>> Technologies >>>> Georgia Institute of Technology >>>> 258 Fourth Street, Rich Building, Room 326 >>>> Atlanta, GA 30332-0700 >>>> Office: (404) 385-0665 >>>> >>>> >>>> >>>> >>>> On Jun 7, 2012, at 2:04 PM, Langhorst, Brad wrote: >>>> >>>>> Mehmet: >>>>> >>>>> It's not important how the files get there, they could be moved >>>>> via ftp, scp, cp, smb - whatever. >>>>> Galaxy will use that directory to import from no matter how the >>>>> files arrive. >>>>> >>>>> I found that confusing at first too. >>>>> >>>>> Brad >>>>> On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote: >>>>> >>>>>> Hi Everyone, >>>>>> >>>>>> I am helping a research group to use Galaxy on our clusters. >>>>>> Unfortunately I have no previous experience with Galaxy, but >>>>>> learning along the way. We are almost there, but cannot figure >>>>>> out one particular issue. This is about configuration of Galaxy, >>>>>> so I thought developers list is a better place to submit than the >>>>>> user list. >>>>>> >>>>>> The galaxy web interface allows for either copy/paste of text, or >>>>>> a URL. Unfortunately we cannot setup a FTP server as instructed >>>>>> due to restrictions on the cluster. The files we are trying to >>>>>> upload are large; around 2GB in size. It does not make sense to >>>>>> upload th
