[galaxy-dev] I can't impersonate an user

[Perez, Ricardo]

Dear all,

We are currently using the stable build of Galaxy and we are encountering the 
following problem:

When we try to impersonate an user, the user drop down menu hangs in looking up 
the user.
In consequence, we can not impersonate the user.

This behaviour started when we upgraded to the Feb 10, 2014 version.

Do we have to modify a configuration file to make this to work again?

Thank you all,
--Ricardo Perez
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Re: [galaxy-dev] Error when searching for tools in local instance.

[Perez, Ricardo]

Hi Sam,

No it did not fix the issue.  When I checked we were in fact in the stable 
branch.

I am sorry for my delayed response,
--Ricardo Perez

- Original Message -
From: "sam guerler" 
To: "Ricardo Perez" 
Cc: "Galaxy-dev Galaxy-dev" 
Sent: Friday, January 24, 2014 5:21:56 PM
Subject: Re: [galaxy-dev] Error when searching for tools in local instance.


Hey Ricardo, 


Did that fix your issue? Does the problem occur in one of the branches? If yes, 
please let me know which one. 


Thanks, 
Sam 



On Wed, Jan 22, 2014 at 10:51 AM, Perez, Ricardo < ricky_...@neo.tamu.edu > 
wrote: 


Hello Sam, 

I believe we are using the default branch. 
I will try to change branches now. 

Thank you, 
--Ricardo Perez 



- Original Message - 
From: "sam guerler" < aysam.guer...@gmail.com > 
To: "Ricardo Perez" < ricky_...@neo.tamu.edu > 
Cc: "Galaxy-dev Galaxy-dev" < galaxy-dev@lists.bx.psu.edu > 
Sent: Tuesday, January 21, 2014 3:19:07 PM 
Subject: Re: [galaxy-dev] Error when searching for tools in local instance. 


Hi Ricardo, 


Are you using the newest version from the stable branch or from default? 


Thanks, 
Sam 



On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo < ricky_...@neo.tamu.edu > 
wrote: 


Dear All, 

When I go to my Galaxy Distibution I go the following place: 
Admin -> Manage installed tool shed repositories 

When I search for a tool in here with the provided search bar, I get the 
following (I believe this is a bug): 

URL: 
https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&f-deleted=False&f-free-text-search=search
 
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 
line 149 in __call__ 
app_iter = self.application(environ, sr_checker) 
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
 line 84 in __call__ 
return self.application(environ, start_response) 
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
 line 633 in __call__ 
return self.application(environ, start_response) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 
in __call__ 
return self.handle_request( environ, start_response ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 
in handle_request 
body = method( trans, **kwargs ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
229 in decorator 
return func( self, trans, *args, **kwargs ) 
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 153 in browse_repositories 
return self.installed_repository_grid( trans, **kwd ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 138 in __call__ 
query = column.filter( trans, trans.user, query, column_filter ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 616 in filter 
clause_list.append( column.get_filter( trans, user, column_filter ) ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 400 in get_filter 
return self.get_single_filter( user, column_filter ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 413 in get_single_filter 
if self.key.find( '.' ) > -1: 
AttributeError: 'NoneType' object has no attribute 'find' 

How would I go to fix this. 

Thank you, 
--Ricardo Perez 
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Re: [galaxy-dev] Error when searching for tools in local instance.

[Perez, Ricardo]

Hello Sam,

I believe we are using the default branch.
I will try to change branches now.

Thank you,
--Ricardo Perez

- Original Message -
From: "sam guerler" 
To: "Ricardo Perez" 
Cc: "Galaxy-dev Galaxy-dev" 
Sent: Tuesday, January 21, 2014 3:19:07 PM
Subject: Re: [galaxy-dev] Error when searching for tools in local instance.


Hi Ricardo, 


Are you using the newest version from the stable branch or from default? 


Thanks, 
Sam 



On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo < ricky_...@neo.tamu.edu > 
wrote: 


Dear All, 

When I go to my Galaxy Distibution I go the following place: 
Admin -> Manage installed tool shed repositories 

When I search for a tool in here with the provided search bar, I get the 
following (I believe this is a bug): 

URL: 
https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&f-deleted=False&f-free-text-search=search
 
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 
line 149 in __call__ 
app_iter = self.application(environ, sr_checker) 
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
 line 84 in __call__ 
return self.application(environ, start_response) 
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
 line 633 in __call__ 
return self.application(environ, start_response) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 
in __call__ 
return self.handle_request( environ, start_response ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 
in handle_request 
body = method( trans, **kwargs ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
229 in decorator 
return func( self, trans, *args, **kwargs ) 
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 153 in browse_repositories 
return self.installed_repository_grid( trans, **kwd ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 138 in __call__ 
query = column.filter( trans, trans.user, query, column_filter ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 616 in filter 
clause_list.append( column.get_filter( trans, user, column_filter ) ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 400 in get_filter 
return self.get_single_filter( user, column_filter ) 
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 413 in get_single_filter 
if self.key.find( '.' ) > -1: 
AttributeError: 'NoneType' object has no attribute 'find' 

How would I go to fix this. 

Thank you, 
--Ricardo Perez 
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[galaxy-dev] Error when searching for tools in local instance.

[Perez, Ricardo]

Dear All,

When I go to my Galaxy Distibution I go the following place:
Admin -> Manage installed tool shed repositories

When I search for a tool in here with the provided search bar, I get the 
following (I believe this is a bug):

URL: 
https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=false&sort=name&page=1&show_item_checkboxes=false&f-deleted=False&f-free-text-search=search
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', 
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
 line 84 in __call__
  return self.application(environ, start_response)
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
 line 633 in __call__
  return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 
in __call__
  return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 
in handle_request
  body = method( trans, **kwargs )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
229 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 153 in browse_repositories
  return self.installed_repository_grid( trans, **kwd )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 138 in __call__
  query = column.filter( trans, trans.user, query, column_filter )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 616 in filter
  clause_list.append( column.get_filter( trans, user, column_filter ) )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 400 in get_filter
  return self.get_single_filter( user, column_filter )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', 
line 413 in get_single_filter
  if self.key.find( '.' ) > -1:
AttributeError: 'NoneType' object has no attribute 'find'

How would I go to fix this.

Thank you,
--Ricardo Perez
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[galaxy-dev] Velvet optimizer: Running two long paired files.

[Perez, Ricardo]

Dear all,

Today when running velvet oprimizer vlsci, we encountered that if you use two 
long files as input then the output is a file that its description is "no 
peek".  However when I run the files seperately the velvet optimizer seems to 
work fine.  I am not sure if this is a bug or not.

Thank you for your time,
--Ricardo Perez
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[galaxy-dev] Velvet optimizer problems : Urgent help.

[Perez, Ricardo]

Dear all,

When trying to run velvet optimizer in galaxy, all the files we get return the 
following:

"No peek"

When looking at the output of galaxy, we get the following:

galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished: 
perl 
/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser/velvet_optimiser_wrapper_vlsci.pl
 '19' '23' '2'  '0' 'short' 'False' 
'' 
'/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2067.dat''not_shortMP''other:''no_amos''not_verbose'
 
'/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2665.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2666.dat'
 
'/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2667.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2663.dat'
 
'/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2668.dat' > 
/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2664.dat

galaxy.jobs.runners DEBUG 2013-07-31 09:31:47,027 executing external set_meta 
script for job 1983: /usr/local/galaxy/galaxy-dist/set_metadata.sh 
./database/files 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983 . 
/usr/local/galaxy/galaxy-dist/universe_wsgi.ini 
/usr/local/galaxy/galaxy-dist/database/tmp/tmp3460Jz 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/galaxy.json
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3117_enOT5T,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3117_vy3tDq,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3117_IFmVK8,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3117_0j3kza,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_over!
 ride_HistoryDatasetAssociation_3117_zwMKHf 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3116_YppZ1L,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3116_Sniis0,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3116_l9RPFx,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3116_It8rUk,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3116_AwvXlS
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3115_TOhpBs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3115_wUomyo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_Histo!
 ryDatasetAssociation_3115_nsUrJl,/usr/local/galaxy/galaxy-dist!
 /databas
e/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3115_DAmGEt,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3115_hFGdc0
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3114_59uEii,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3114_UcezIt,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3114_YmOlHD,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3114_owVBfP,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3114_O3UH82
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3113_vMrQrs,/usr/local/galaxy/galaxy-dist/database/!
 
job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3113_YhwIGZ,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3113_pAG6wP,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3113_9ImAZ6,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3113_uI5cbM
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3112_NwB9j6,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3112_LK2cWo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3112__FDnXW,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDa

[galaxy-dev] Bowtie2 error: Creates a 62 kb file.

[Perez, Ricardo]

Dear all,

Today we ran some problems when running bowtie2.  When we run bowtie2, the run 
manages to complete.  However, bowtie2 creates a 62kb file.
The error log that we get is the following:

galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination 
(destination id: local:///)
galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched
galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command 
for dependency 'bowtie2'
galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 
'bowtie2', ignoring
galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command 
for dependency 'samtools'
galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 
'samtools', ignoring
galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: 
bowtie2 --version &> 
/usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python 
/usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py   
   --num-threads="4"  
--output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat  
 
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12"
  --single-paired=paired  
--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat  

--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat  
   -I 0 -X 250  --settings=preSet
galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination 
(destination id: local:///)
galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: 
bowtie2 --version &> 
/usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python 
/usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py   
   --num-threads="4"  
--output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat  
 
--indexes-path="/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12"
  --single-paired=paired  
--input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat  

--input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat  
   -I 0 -X 250  --settings=preSet
galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta 
script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh 
./database/files 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . 
/usr/local/galaxy/galaxy-dist/universe_wsgi.ini 
/usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/galaxy.json
 
/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAssociation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_results_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_over!
 ride_HistoryDatasetAssociation_1767_MZilrL
165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] "GET 
/api/histories/ca8efa3c47500414 HTTP/1.1" 200 - 
"http://galaxy.tamu.edu/history"; "Mozilla/5.0 (X11; Linux x86_64) 
AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 
Chrome/25.0.1364.160 Safari/537.22"
165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET /history HTTP/1.1" 200 - 
"http://galaxy.tamu.edu/tool_runner/index"; "Mozilla/5.0 (Macintosh; Intel Mac 
OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 
Safari/537.36"
165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET 
/api/histories/1ab12f1e464820dd HTTP/1.1" 200 - 
"http://galaxy.tamu.edu/history"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 
10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 
Safari/537.36"
165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] "GET 
/history/get_display_application_links HTTP/1.1" 200 - 
"http://galaxy.tamu.edu/history"; "Mozilla/5.0 (Macintosh; Intel Mac OS X 
10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 
Safari/537.36"
galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external 
set_meta for job 1483 finished
galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata from 
file for: HistoryDatasetAssociation 1767

We currently have the most recent version of bowtie2 and samtools.  Anyone know 
how to fix this?

Thank you for your time,
--Ricardo Perez

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Re: [galaxy-dev] Trackster and bedtools error

[Perez, Ricardo]

Thank you for your quick response.  However, I have checked and bedtools are 
indeed in the galaxy path.  When reviewind the log, I get the following:

galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution
finished: grep -v '^#'
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_515.dat |
sort -k1,1 |   bedtools genomecov -bg -split -i stdin -g
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
   > temp.bg ; bedGraphToBigWig temp.bg
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_519.dat

After reading the log, I ran the following command in my terminal:

bedtools genomecov -bg -split -i stdin -g 
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len

However this crashes.  After looking in my computer, I find that bedtools do 
not contain the file genomecov.  Is this an erroneous assumption of mine or 
have I installed something wrong?

Than you for your time,
--Ricardo Perez
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[galaxy-dev] Trackster and bedtools error

[Perez, Ricardo]

Dear all,

As I was trying to do visualize my data set in trackster, I get the following 
error:

/bin/sh: 1: bedtools: not found
sort: fflush failed: standard output: Broken pipe
sort: write error
needLargeMem: trying to allocate 0 bytes (limit: 1000)

When doing a sudo find / -name "bedtools" in my system, I get the following 
output:
/usr/share/bedtools 
/usr/share/doc/bedtools

Do I have bedtools installed in the wrong place?

Thank you for your help,
--Ricardo Perez
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[galaxy-dev] How were liftover and nib files generated?

[Perez, Ricardo]

Dear all,

When I rsync files from let say the following command:
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/dm3 .

The system will sync files that are related to genome aligments, liftover, and 
nibs.
How did the Galaxy team generated this files?
The reason I ask is because I would lather will like to generate similar files 
to custom genomes to be used in galaxy.

Thank you for your time,
--Ricardo Perez
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[galaxy-dev] Question about bowtie2_indeces.loc

[Perez, Ricardo]

Dear all,
When adding a genome I understand that the format are added in the following 
way:

   

My question is, what is the difference between the unique_build_id and the 
dbkey?

Thank you for your time,
--Ricardo Perez
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[galaxy-dev] Configuring the time of permanently deleting data sets.

[Perez, Ricardo]

Dear all,

I am currently trying to find a way to decrease the time the users need to wait 
to permanently delete their data sets.  In galaxy I read the following 
"Histories that have been deleted for more than a time period specified by the 
Galaxy administrator(s) may be permanently deleted."; I am wondering where can 
I configure this option in my local instance of galaxy. I have looked for such 
an option in the universe_wsgi.ini file but I have not found it.  I would 
greatly appreciate if someone can point me to the right direction to modify 
this.

Thank you all,
--Ricardo Perez
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[galaxy-dev] Error in using Trackster: datatypes_conf.xml

[Perez, Ricardo]

Dear all,

I am trying to set up trackster for my local instance in galaxy.  I did the 
following:

Uncommented from the universe_wsgi.ini;
len_file_path = path/to/file/galaxy-dist/tool-data/shared/ucsc/chrom

Also I ran the following commands:

mkdir ./tool-data/shared/ucsc/chrom/
python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/

However when I try to use trackster, I get the following message:

"A converted for this file is not installed. Please heck your 
datatypes_conf.xml file."

How exactly do I find out which converted files I am missing?  I did the above 
steps in another instance of galaxy and Trackster works fine in there.

Thank you for your time,
--Ricardo Perez
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[galaxy-dev] Initial display with Simulate (version 1.0.0)

[Perez, Ricardo]

Dear all,

When running Simulate (version 1.0.0)I am missing a graph in the initial 
display.  Is this a bug or is it my instance problem.  On a side note, when 
running Simulate I found out that if you don't place parameters in 
"Frequency/ies for minor allele:" and "Detection thresholds:" the job will 
fail.  It would be nice to indicate that those parameters are a must for 
running the tool.

Thank you,
--Ricardo Perez 
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Re: [galaxy-dev] ProFTPD integration with Galaxy

[Perez, Ricardo]

I am sorry, i posted the wrong configuration file above.  I am posting now the 
updated proftpd.conf , the differences is that some things are commented out 
and others are not.

# This is a basic ProFTPD configuration file (rename it to 
# 'proftpd.conf' for actual use.  It establishes a single server
# and a single anonymous login.  It assumes that you have a user/group
# "nobody" and "ftp" for normal operation and anon.

ServerName  "Genomics01 ProFTPd"
ServerType  standalone
DefaultServer   on
DeferWelcomeoff
UseIPv6 on
IdentLookupsoff
MultilineRFC2228on
ShowSymlinkson

ModulePath  
/usr/local/galaxy/downloads/proftpd-1.3.5rc3/modules/

LoadModule  mod_sql.c
LoadModule  mod_sql_postgres.c
LoadModule  mod_sql_passwd.c


SQLBackend  postgres
SQLEngine   on
SQLAuthenticate users
SQLAuthTypesSHA1 SHA256 pbkdf2
SQLPasswordPBKDF2   SHA256 1000 24
#SQLPasswordSaltFile/path/to/file
SQLConnectInfo  galaxydb@localhost:5432 ftpuser mypassword
SQLUserInfo custom:/LookupGalaxyUser
#SQLNamedQuery  LookupGalaxyUser SELECT 
"email,password,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'"

SQLPasswordUserSalt sql:/GetUserSalt


SQLNamedQuery   LookupGalaxyUser  SELECT "email, (CASE WHEN 
substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 
69) ELSE password END) AS 
password2,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'"

SQLNamedQuery   GetUserSalt SELECT "(CASE WHEN SUBSTRING 
(password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) 
END) AS salt FROM galaxy_user WHERE email='%U'"




SQLDefaultGID   1002
SQLDefaultUID   1002

TimeoutNoTransfer   600
TimeoutStalled  600
TimeoutIdle 1200

DisplayLoginwelcome.msg
DisplayChdir.message true
ListOptions "-l"

DenyFilter  \*.*/

# Use this to jail all users in their homes
DefaultRoot ~
CreateHome  on dirmode 700
AllowOverwrite  on
AllowStoreRestart   on
SQLPasswordEngine   on
SQLPasswordEncoding hex
PassivePorts  3 4



# Port 21 is the standard FTP port.
Port21

# Don't use IPv6 support by default.
# Umask 022 is a good standard umask to prevent new dirs and files
# from being group and world writable.
Umask   077

# To prevent DoS attacks, set the maximum number of child processes
# to 30.  If you need to allow more than 30 concurrent connections
# at once, simply increase this value.  Note that this ONLY works
# in standalone mode, in inetd mode you should use an inetd server
# that allows you to limit maximum number of processes per service
# (such as xinetd).
MaxInstances30

# Set the user and group under which the server will run.
Usergalaxy
Group   galaxy

# To cause every FTP user to be "jailed" (chrooted) into their home
# directory, uncomment this line.
#DefaultRoot ~

# Normally, we want files to be overwriteable.
AllowOverwrite  on

AuthOrder   mod_sql.c


# Bar use of SITE CHMOD by default
#
#  DenyAll
#
Include /etc/proftpd/conf.d/
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Re: [galaxy-dev] ProFTPD integration with Galaxy

[Perez, Ricardo]

Hi Mr. Tobias,

We are having a similar problem.  It seems that when the galaxy code was 
updates, new created/updated passwords are using a different encryption mode.  
This new mode, PBKDF2 SHA256 is NOT supported by proftpd 1.3.4d that you see to 
be using. We had to compile proftpd from source since version 1.3.5rc3 does 
support this encryption. Now in the password 
PBKDF2$sha256$1$8h/4HmD1Eu6NTc7F$Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh I was 
able to deduce the following by reading the code from git hub "password.py".  
The encrypted password is acually Slb1H5a9YJvR6A3cUnZCUfh7tOWKfRuh where the 
salt is 8h/4HmD1Eu6NTc7F using PBKDF2 SHA256 with an illiteration value of 
1.  The most importnat part is that the salt, is right there, from 
character 21 to 36. With the newly compiled proftpd, I have the following 
configuration at proftpd.conf:


# This is a basic ProFTPD configuration file (rename it to 
# 'proftpd.conf' for actual use.  It establishes a single server
# and a single anonymous login.  It assumes that you have a user/group
# "nobody" and "ftp" for normal operation and anon.

ServerName  "Genomics01 ProFTPd"
ServerType  standalone
DefaultServer   on
DeferWelcomeoff
UseIPv6 on
IdentLookupsoff
MultilineRFC2228on
ShowSymlinkson

ModulePath  
/usr/local/galaxy/downloads/proftpd-1.3.5rc3/modules/

LoadModule  mod_sql.c
LoadModule  mod_sql_postgres.c
LoadModule  mod_sql_passwd.c


SQLBackend  postgres
SQLEngine   on
SQLAuthenticate users
SQLAuthTypesSHA1 SHA256 pbkdf2
SQLPasswordPBKDF2   SHA256 1000 24
#SQLPasswordSaltFile/path/to/file
SQLConnectInfo  galaxydb@localhost:5432 ftpuser mypassword
SQLUserInfo custom:/LookupGalaxyUser
SQLNamedQuery   LookupGalaxyUser SELECT 
"email,password,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'"

SQLPasswordUserSalt sql:/GetUserSalt


SQLNamedQuery   LookupGalaxyUser  SELECT "email, (CASE WHEN 
substring(password from 1 for 6) = 'PBDKF2' THEN substring(password from 38 for 
69) ELSE password END) AS 
password2,'galaxy','galaxy','/usr/local/galaxy/galaxy-dist/database/ftp/%U','/bin/bash'
 FROM galaxy_user WHERE email='%U'"

SQLNamedQuery   GetUserSalt SELECT "(CASE WHEN SUBSTRING 
(password from 1 for 6) = 'PBDKF2' THEN SUBSTRING (password from 21 for 36) 
END) AS salt FROM galaxy_user WHERE email='%U'"




SQLDefaultGID   1002
SQLDefaultUID   1002

TimeoutNoTransfer   600
TimeoutStalled  600
TimeoutIdle 1200

DisplayLoginwelcome.msg
DisplayChdir.message true
ListOptions "-l"

DenyFilter  \*.*/

# Use this to jail all users in their homes
DefaultRoot ~
CreateHome  on dirmode 700
AllowOverwrite  on
AllowStoreRestart   on
SQLPasswordEngine   on
SQLPasswordEncoding hex
PassivePorts  3 4



# Port 21 is the standard FTP port.
Port21

# Don't use IPv6 support by default.
# Umask 022 is a good standard umask to prevent new dirs and files
# from being group and world writable.
Umask   077

# To prevent DoS attacks, set the maximum number of child processes
# to 30.  If you need to allow more than 30 concurrent connections
# at once, simply increase this value.  Note that this ONLY works
# in standalone mode, in inetd mode you should use an inetd server
# that allows you to limit maximum number of processes per service
# (such as xinetd).
MaxInstances30

# Set the user and group under which the server will run.
Usergalaxy
Group   galaxy

# To cause every FTP user to be "jailed" (chrooted) into their home
# directory, uncomment this line.
#DefaultRoot ~

# Normally, we want files to be overwriteable.
AllowOverwrite  on

#AuthOrder   mod_sql.c


# Bar use of SITE CHMOD by default
#
#  DenyAll
#
Include /etc/proftpd/conf.d/



With the configuration above, I can still connect to users that have SHA1 
passwords, but I think I need a little more tweeking to get it to work with the 
new passwords.

Best,
--Ricardo Perez
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[galaxy-dev] Error in universe_wsgi.ini regarding gzip

[Perez, Ricardo]

Dear all,

I have encountered a problem where my browser does not show the history sidebar 
in galaxy.  In my configuration I had the following line in universe_wsgi.ini 
uncommented, which seem to be the source of the problem. 

#filter-with = gzip

Commenting that line will fix my browser and see the history bar again.

Thanks,
--Ricardo Perez
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[galaxy-dev] Errors when starting galaxy

[Perez, Ricardo]

Dear all,

I get the following errors when starting galaxy, is there any way to fix this.

Error loading display application (./display_applications/genetrack.xml): 
[Errno 2] No such file or directory: './display_applications/genetrack.xml'
Traceback (most recent call last):
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 
498, in load_display_applications
display_app = DisplayApplication.from_file( config_path, self )
  File 
"/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py",
 line 163, in from_file
return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry )
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, 
in parse_xml
tree = ElementTree.parse(fname)
  File 
"/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
 line 859, in parse
tree.parse(source, parser)
  File 
"/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
 line 576, in parse
source = open(source, "rb")



Error loading display application (./display_applications/genetrack.xml): 
[Errno 2] No such file or directory: './display_applications/genetrack.xml'
Traceback (most recent call last):
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", line 
498, in load_display_applications
display_app = DisplayApplication.from_file( config_path, self )
  File 
"/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py",
 line 163, in from_file
return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry )
  File "/usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 143, 
in parse_xml
tree = ElementTree.parse(fname)
  File 
"/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
 line 859, in parse
tree.parse(source, parser)
  File 
"/usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py",
 line 576, in parse
source = open(source, "rb")

Best,

--Ricardo Perez
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[galaxy-dev] How to distribute our local installation via git(logistics)

[Perez, Ricardo]

Hello,

We want to able to distribute Galaxy configured with the UCSC browser, 
specially for people who are not too UNIX savvy.  We had a question on how to 
do this, since we are planning to do it via git.  How can we set up the git 
server, in such a way that it doesn't compromise important files that are 
specific to our installation.  For example, in our universe_wsgi.ini file we 
have passwords for our database that we do not want to distribute.  However, we 
do want to distribute universe_wsgi.ini in releases so people can be updated in 
important changes.  We were thinking that maybe we should have a test machine 
to make sure all the changes does not break Galaxy, and then push the changes 
to our server machine an to our git server.  However, we are not sure if this 
is the most efficient way to do it.  Does anyone know how we can accomplish 
this without complicating too many things?

Thank you for your time and patience,
--Ricardo Perez
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[galaxy-dev] Error when trying to display data on gene track

[Perez, Ricardo]

Hello,

We are running a local instance of galaxy and we get the following error when 
trying to display genes from our history in the ucsc browser.  I got the error 
as I was following the galaxy 101 video in the galaxy website (last step).

Thanks,
--Ricardo Perez

URL: 
http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797
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:132 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:185 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application
>>  display_link = display_app.get_link( link_name, data, dataset_hash, 
>> user_hash, trans )
Module galaxy.datatypes.display_applications.application:189 in get_link
>>  return PopulatedDisplayApplicationLink( self.links[ link_name ], data, 
>> dataset_hash, user_hash, trans )
Module galaxy.datatypes.display_applications.application:129 in __init__
>>  self.ready, self.parameters = self.link.build_parameter_dict( self.data, 
>> self.dataset_hash, self.user_hash, trans )
Module galaxy.datatypes.display_applications.application:66 in
build_parameter_dict
>>  if param.ready( other_values ):
Module galaxy.datatypes.display_applications.parameters:119 in ready
>>  raise Exception( 'A data display parameter is in the error state: %s' % ( 
>> self.name ) )
Exception: A data display parameter is in the error state: genetrack_file
extra data

full traceback
URL: 
http://galaxy.tamu.edu/dataset/display_application?user_id=None&app_name=genetrack_interval&link_name=genetrack&dataset_id=b938ed79e37fc797
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:132 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:185 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application
>>  display_link = display_app.get_link( link_name, data, dataset_hash, 
>> user_hash, trans )
Module galaxy.datatypes.display_applications.application:189 in get_link
>>  return PopulatedDisplayApplicationLink( self.links[ link_name ], data, 
>> dataset_hash, user_hash, trans )
Module galaxy.datatypes.display_applications.application:129 in __init__
>>  self.ready, self.parameters = self.link.build_parameter_dict( self.data, 
>> self.dataset_hash, self.user_hash, trans )
Module galaxy.datatypes.display_applications.application:66 in
build_parameter_dict
>>  if param.ready( other_values ):
Module galaxy.datatypes.display_applications.parameters:119 in ready
>>  raise Exception( 'A data display parameter is in the error state: %s' % ( 
>> self.name ) )
Exception: A data display parameter is in the error state: genetrack_file
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[galaxy-dev] Extract genomic DNA job error

[Perez, Ricardo]

Hello,

I am getting this error when using Extract Genomic DNA (version 2.2.2)

empty
format: fasta, database: hg19
924 warnings, 1st is: Chromosome by name 'chr22' was not found for build 
'hg19'. Skipped 924 invalid lines, 1st is #1, "chr22   1625633116287937 
NM_001136213   0   -   16258185 16287885   0   11 
346,119,167,45,71,71,138,107,174,115,684, 0,1853,10597,11805,13541,188

We set up a local instance of Galaxy and a local mirror of the UCSC Table 
browser in our servers.

Thank you for your help,
--Ricardo Perez
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[galaxy-dev] Database source

[Perez, Ricardo]

Hello Galaxy,

We are implementing a fresh instance of Galaxy in the school server for 
teaching purposes.  So obtaining genomic data from the UCSC servers can present 
a problem by overloading the connection.  To make things faster, we want to 
obtain the data for the genomic data and have it in our servers, speeding up 
data retrieval.  At first I was under the impression that we had to use MySQL 
for this, and downloaded MySQL files from the UCSC servers by using:

$ rsync -avzP rsync:// hgdownload.cse.ucsc.edu/mysql .

We have successfully added the data to MySQL in our server, but now do not know 
how to make galaxy see the data.  However after searching more about the 
problem, I found out that I could have used the following instead:

$ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ .

Was downloading the mysql files unnecessary or can I still be able to use them? 
Also, would it be more efficient to use the second rsync option instead?

Thank you for your help,
--Ricardo Perez
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[galaxy-dev] (no subject)

[Perez, Ricardo]

Hi, 
We are having problems fetching sequences from our mysql database to galaxy. 
Does anyone know how to do so? 
Thank you for your help. 
--Ricardo Perez. 

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[galaxy-dev] Local Instance permissions.

[Perez, Ricardo]

Hi,

We are implementing a local instance of Galaxy and I had a quick question, is 
it wrong to give Galaxy access to the UCSC databases?

Thank you for your time and patience,
--Ricardo Perez
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[galaxy-dev] Local data

[Perez, Ricardo]

Hi,

I am sorry for the trivial question.  Does anyone know how I can make a local 
instance of Galaxy use our local database files?  We have downloaded the 
database from USCS and would like to use the downloaded files instead of 
retrieving it from the UCSC Table Browser when processing data.  

Thank you very much for your help,
--Ricardo Perez
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[galaxy-dev] Downloading UCSC complete database

[Perez, Ricardo]

Dear all,

I am currently working on downloading the genome data from the UCSC database.
I have figured out how to obtain the genome of one species at a time, however 
this would take a bit of time if I have to type every command by hand.
Is there any command that would download the all the data from the UCSC 
databases?
If not, how would I go to start in writing a script that would do so.

Thank you for your time.
-Ricardo
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