Seems like an error concerning permissions in your galaxy folders. Try:

sudo chmod 777 galaxy-dist/

and then try to upload data again.

To: galaxy-dev@bx.psu.edu From: liisa.koski@dnalandmarks.ca Date: Tue, 20 Dec 2011 16:22:02 -0500 Subject: [galaxy-dev] Problem uploading files from filesystem paths

Hi,

I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error.

Any ideas?

Thanks in advance,

Liisa

Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, js

Job Standard Error

Traceback (most recent call last):

File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in

__main__()

File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__

add_file( dataset, registry, json_file, output_path )

File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 300, in add_file

if datatype.dataset_content_needs_grooming( dataset.path ):

File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming

version = self._get_samtools_version()

File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version

output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1]

File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__

errread, errwrite)

File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child

raise child_exception

OSError: [Errno 13] Permission denied

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If the following config setting is set to True in universe_wsgi.ini, then the event messages will be logged to the message column of the Event table in the Galaxy database.

# Log events log_events = False

On Dec 27, 2011, at 1:32 PM, Alfonso Núñez Salgado wrote:

Hi,

I'm trying to understand the galaxy code to solve a previewing issue and I'd like to know where "trans.log_event" method writes the log. Is there any diagram, schema or any developing documentation?

Thanks in advance ___________________________________________________________ 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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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

Thanks Greg,

This option is set to True in my universe_wsgi.ini, but paster.log still not showing this kind of messages.

Log Option configuration:

log_level = DEBUG database_engine_option_echo = False log_events = True log_actions = True debug = True use_printdebug = True use_interactive = True use_heartbeat = False

On 27/12/11 20:15, Greg Von Kuster wrote:

If the following config setting is set to True in universe_wsgi.ini, then the event messages will be logged to the message column of the Event table in the Galaxy database.

# Log events log_events = False

On Dec 27, 2011, at 1:32 PM, Alfonso Núñez Salgado wrote:

...

Hi,

I'm trying to understand the galaxy code to solve a previewing issue and I'd like to know where "trans.log_event" method writes the log. Is there any diagram, schema or any developing documentation?

Thanks in advance ___________________________________________________________ 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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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu mailto:greg@bx.psu.edu

Hello Ted,

I assume you cloned your local Galaxy instance from our distribution repo at https://bitbucket.org/galaxy/galaxy-dist.

Unfortunately, in order to make use of the features that enable communication between your local Galaxy instance and a Galaxy tool shed, you have to update your local Galaxy instance from our Galaxy central repo at https://bitbucket.org/galaxy/galaxy-central. This is because the distribution repo is not updated as often as is necessary to keep current with the rapidly evolving tool shed code base and feature set. This issue should be eliminated at some point.

On Dec 27, 2011, at 11:54 PM, Ted Goldstein wrote:

Hello, I just installed Galaxy and am very impressed. But I am having problems adding in tools from the toolshed. When I click on adding a tool such as the Venn Diagram tool, it brings up the following message (even though I never installed it before:

============ Found

The resource was found at xyzzy.ucsc.edu:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=9956e395db5a106ba074ae610c5...; you should be redirected automatically. WSGI Server =================

The page never redirects. As well the URL is malformed (missing the "http:"). If I fabricate this by hand. E.g. http://xyzzy.ucsc.edu:1234/admin_toolshed/install_repository?tool_shed_url=h...

============ Not Found

The resource could not be found. No route for /admin_toolshed/install_repository ============ The log file shows: .2.3.4 - - [27/Dec/2011:20:33:27 -0700] "GET /admin/browse_tool_sheds HTTP/1.1" 200 - "http://xyzzy.ucsc.edu:1234/admin" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25) Gecko/20111212 Firefox/3.6.25" 1.2.3.4 - - [27/Dec/2011:20:33:30 -0700] "GET /admin/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.1" 302 - "http://xyzzy.ucsc.edu:1234/admin/browse_tool_sheds" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25) Gecko/20111212 Firefox/3.6.25" 1.2.3.4 - - [27/Dec/2011:20:44:28 -0700] "GET /admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu&repo_info_dict=9956e395db5a106ba074ae610c5... HTTP/1.1" 404 - "-" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25) Gecko/20111212 Firefox/3.6.25"

===============

I looked through the mailing list and wiki and I don't see this problem. Could I have misinstalled or misconfigured something?

Thanks for the great system!

Best regards, Ted

Ted Goldstein ted@soe.ucsc.edu Ph.D. Candidate, HausslerLab, CBSE, UCSC (650) 743-4141 http://soe.ucsc.edu/~ted

---

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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

On Dec 21, 2011, at 3:48 AM, Makis Ladoukakis wrote:

Seems like an error concerning permissions in your galaxy folders. Try:

sudo chmod 777 galaxy-dist/

and then try to upload data again.

Setting world-writable should be considered a last resort in any scenario. The problem here seems to be that samtools can't be executed. Is it installed on whatever system is executing the upload tool?

--nate

To: galaxy-dev@bx.psu.edu From: liisa.koski@dnalandmarks.ca Date: Tue, 20 Dec 2011 16:22:02 -0500 Subject: [galaxy-dev] Problem uploading files from filesystem paths

Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas?

Thanks in advance, Liisa

Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied

___________________________________________________________ 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/ ___________________________________________________________ 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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