[galaxy-dev] Galaxy cannot start last [server:handlerxx]

2013-08-09 Thread Rodolfo Aramayo 
On Thu, Aug 8, 2013 at 1:31 PM, Nate Coraor n...@bx.psu.edu wrote:
 On Aug 5, 2013, at 6:23 PM, Rodolfo Aramayo wrote:

 Hi,

 I have a 80 core/1TB RAM Dell server.
 In order improve Galaxy performance I modified the universe_wsgi.ini
 file so as to improve the Scaling and Load Balancing
 as follows:

 # Use a threadpool for the web server instead of creating a thread for each
 # request.
 use_threadpool = True

 # Number of threads in the web server thread pool.
 threadpool_workers = 200

 
 [server:web0]
 use = egg:Paste#http
 port = 8090
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 ... snip ...

 [server:handler18]
 use = egg:Paste#http
 port = 8318
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 # [server:handler19]
 # use = egg:Paste#http
 # port = 8319
 # host = 127.0.0.1
 # use_threadpool = true
 # threadpool_workers = 5

 # [server:handler20]
 # use = egg:Paste#http
 # port = 8320
 # host = 127.0.0.1
 # use_threadpool = true
 # threadpool_workers = 5

 
 job_manager = manager
 job_handlers = 
 handler0,handler1,,handler2,handler3,handler4,handler5,handler6,handler7,handler8,handler9,handler10,handler11,handler12,handler13,handler14,handler15,handler16,handler17,handler18

 Hi Rodolfo,

 The job_manager and job_handlers options go under the [server:main] section, 
 it looks like they are probably underneath the last [server:...] section 
 right now.

 Please note that all of these features should now be configured via the job 
 configuration file (job_conf.xml), and I've just updated the documentation 
 you referred to accordingly.

 --nate

Dear Nate,

Thanks

Just to be sure I understand this correctly

I now have in my 'universe' file the following:

#
#  HTTP Server
--

# Configuration of the internal HTTP server.

[server:main]

# job_manager = manager  I ASSUME THIS IS CORRECT because I get
errors when it is not  commented



[server:manager]
use = egg:Paste#http
port = 8200
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5



[server:handler0]
use = egg:Paste#http
port = 8300
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler1]
use = egg:Paste#http
port = 8301
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

...snip...

[server:handler19]
use = egg:Paste#http
port = 8319
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

# [server:handler20]
# use = egg:Paste#http
# port = 8320
# host = 127.0.0.1
# use_threadpool = true
# threadpool_workers = 5


# The internal HTTP server to use.  Currently only Paste is provided.
This
# option is required.
use = egg:Paste#http

# The port on which to listen.
#port = 8080

# The address on which to listen.  By default, only listen to
localhost (Galaxy
# will not be accessible over the network).  Use '0.0.0.0' to listen
on all
# available network interfaces.
#host = 127.0.0.1
host = 0.0.0.0

# Use a threadpool for the web server instead of creating a thread for
each
# request.
use_threadpool = True

# Number of threads in the web server thread pool.
threadpool_workers = 200


[server:web0]
use = egg:Paste#http
port = 8400
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web1]
use = egg:Paste#http
port = 8401
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

...snip...

[server:web11]
use = egg:Paste#http
port = 8411
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web12]
use = egg:Paste#http
port = 8412
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10


#  Filters --

# Filters sit between Galaxy and the HTTP server.
...

#

And in my job_conf.xml:

handler id=handler0 tags=handlers/
handler id=handler1 tags=handlers/
...snip...
handler id=handler18 tags=handlers/
handler id=handler19 tags=handlers/

#

Is this correct?

Also, I guess the part I do not understand is what is the magic
formula between the number of threadpool_workers as configured here:

# Use a threadpool for the web server instead of creating a thread for
each
# request.
use_threadpool = True

# Number of threads in the web server thread pool.
threadpool_workers = 200

and those configured on the web servers and on the server handlers?

Thanks

--Rodolfo

[galaxy-dev] Galaxy cannot start last [server:handlerxx]

2013-08-09 Thread Rodolfo Aramayo 
It worked like a charm

Thanks

--R

On Fri, Aug 9, 2013 at 12:32 PM, Nate Coraor n...@bx.psu.edu wrote:

 On Aug 9, 2013, at 1:16 PM, Rodolfo Aramayo wrote:

 Dear Nate,

 Thanks

 Just to be sure I understand this correctly

 I now have in my 'universe' file the following:

 #
 #  HTTP Server
 --

 # Configuration of the internal HTTP server.

 [server:main]

 # job_manager = manager  I ASSUME THIS IS CORRECT because I get
 errors when it is not  commented

 

 [server:manager]
 use = egg:Paste#http
 port = 8200
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 

 [server:handler0]
 use = egg:Paste#http
 port = 8300
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler1]
 use = egg:Paste#http
 port = 8301
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 ...snip...

 [server:handler19]
 use = egg:Paste#http
 port = 8319
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 # [server:handler20]
 # use = egg:Paste#http
 # port = 8320
 # host = 127.0.0.1
 # use_threadpool = true
 # threadpool_workers = 5

 
 # The internal HTTP server to use.  Currently only Paste is provided.
 This
 # option is required.
 use = egg:Paste#http

 # The port on which to listen.
 #port = 8080

 # The address on which to listen.  By default, only listen to
 localhost (Galaxy
 # will not be accessible over the network).  Use '0.0.0.0' to listen
 on all
 # available network interfaces.
 #host = 127.0.0.1
 host = 0.0.0.0

 # Use a threadpool for the web server instead of creating a thread for
 each
 # request.
 use_threadpool = True

 # Number of threads in the web server thread pool.
 threadpool_workers = 200

 
 [server:web0]
 use = egg:Paste#http
 port = 8400
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 [server:web1]
 use = egg:Paste#http
 port = 8401
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 ...snip...

 [server:web11]
 use = egg:Paste#http
 port = 8411
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 [server:web12]
 use = egg:Paste#http
 port = 8412
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 
 #  Filters --

 # Filters sit between Galaxy and the HTTP server.
 ...

 #

 And in my job_conf.xml:

handler id=handler0 tags=handlers/
handler id=handler1 tags=handlers/
 ...snip...
   handler id=handler18 tags=handlers/
handler id=handler19 tags=handlers/

 #

 Is this correct?

 Rodolfo,

 Some of this confusion might be because you have the (documented) options 
 from the original [server:main] section orphaned underneath 
 [server:handler19], which already has those options set.  In an ini file, 
 sections begin with [name] and all key/value pairs underneath that heading 
 are assigned to [name] until another section heading is encountered.  
 Removing all comments, that means your config would look like this:

 [server:main]

 [server:manager]
 use = egg:Paste#http
 port = 8200
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler0]
 use = egg:Paste#http
 port = 8300
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler1]
 use = egg:Paste#http
 port = 8301
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler19]
 use = egg:Paste#http
 port = 8319
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5
 use = egg:Paste#http
 host = 0.0.0.0
 use_threadpool = True
 threadpool_workers = 200

 [server:web0]
 use = egg:Paste#http
 port = 8400
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 [server:web1]
 use = egg:Paste#http
 port = 8401
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 [server:web11]
 use = egg:Paste#http
 port = 8411
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 [server:web12]
 use = egg:Paste#http
 port = 8412
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 10

 -

 Remove [server:main], the entire [server:manager] section, and those extra 
 options under [server:handler19], and you should be good:

 [server:handler0]
 use = egg:Paste#http
 port = 8300
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler1]
 use = egg:Paste#http
 port = 8301
 host = 127.0.0.1
 use_threadpool = true
 threadpool_workers = 5

 [server:handler19]
 use = egg:Paste#http
 port = 8319
 host

[galaxy-dev] Error running oasesoptimizer rev. 53e887dda799 (konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)

2013-08-09 Thread Rodolfo Aramayo 
Hi,

Regarding the error I experienced with

[galaxy-dev] Error running oasesoptimizer rev. 53e887dda799
(konradpaszkiewicz) on Galaxy fd4113962c32+ (stable)

Two things:

FIRST
The error I reported, in short, it was my fault as I failed to to set up the:

cmdline = 
'/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh
%s %s \'%s\' %s %s  21/dev/null'

line properly in the oases_optimiser.py script properly

I guess it would help for developers to state exactly the
customization required for each package installed via ToolShed for the
tool to work properly or better yet, it would be really nice if we
could set up environmental variables like:

TOOL_SHED_REPOS=/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos

so that scripts could invoke them upon installation:

cmdline = 
'$TOOL_SHED_REPOS/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.sh
%s %s \'%s\' %s %s  21/dev/null'

SECOND

I still am experiencing errors with this tool

When I run oases_optimiser on either fasta or fastq files the jobs
start, run and then fail
In all cases the problem is the lack of an ''splicing_events.txt' file

Help will be appreciated

Thanks

--R

#
The stderr is as follows:

Traceback (most recent call last):
  File 
/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py,
line 120, in module
if __name__ == __main__: __main__()
  File 
/usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/konradpaszkiewicz/oasesoptimiser/53e887dda799/oasesoptimiser/oases_optimiser.py,
line 76, in __main__
for line in open(path ):
IOError: [Errno 2] No such file or directory: 'splicing_events.txt'


#
The stdout is as follows:

[0.00] Reading FastQ file
/usr/local/galaxy/galaxy-dist/database/files/003/dataset_3687.dat;
[13.354877] 8855297 sequences found
[13.354879] Done
[13.354940] Reading read set file ./Sequences;
[14.405160] 8855297 sequences found
[20.956147] Done
[20.956153] 8855297 sequences in total.
[20.956229] Writing into roadmap file ./Roadmaps...
[23.008558] Inputting sequences...
[23.008571] Inputting sequence 0 / 8855297
[25.835351] Inputting sequence 100 / 8855297
[28.835964] Inputting sequence 200 / 8855297
[31.938277] Inputting sequence 300 / 8855297
[35.129436] Inputting sequence 400 / 8855297
[38.384093] Inputting sequence 500 / 8855297
[41.660153] Inputting sequence 600 / 8855297
[44.905326] Inputting sequence 700 / 8855297
[48.168615] Inputting sequence 800 / 8855297
[50.969068]  === Sequences loaded in 28.188442 s
[50.969101] Done inputting sequences
[50.969103] Destroying splay table
[51.018112] Splay table destroyed
[0.00] Reading roadmap file ./Roadmaps
[13.140830] 8855297 roadmaps read
[13.144978] Creating insertion markers
[15.796233] Ordering insertion markers
[21.652798] Counting preNodes
[22.631404] 2753107 preNodes counted, creating them now
[24.516794] Sequence 100 / 8855297
[25.609456] Sequence 200 / 8855297
[26.585862] Sequence 300 / 8855297
[27.501523] Sequence 400 / 8855297
[28.375045] Sequence 500 / 8855297
[29.217391] Sequence 600 / 8855297
[30.037355] Sequence 700 / 8855297
[30.838062] Sequence 800 / 8855297
[31.514315] Adjusting marker info...
[32.498044] Connecting preNodes
[32.734023] Connecting 100 / 8855297
[33.029694] Connecting 200 / 8855297
[33.36] Connecting 300 / 8855297
[33.712200] Connecting 400 / 8855297
[34.080947] Connecting 500 / 8855297
[34.464629] Connecting 600 / 8855297
[34.853754] Connecting 700 / 8855297
[35.256476] Connecting 800 / 8855297
[35.604610] Cleaning up memory
[35.622205] Done creating preGraph
[35.622208] Concatenation...
[36.944164] Renumbering preNodes
[36.944174] Initial preNode count 2753107
[36.992738] Destroyed 2139761 preNodes
[36.992745] Concatenation over!
[36.992747] Clipping short tips off preGraph
[37.241017] Concatenation...
[37.561728] Renumbering preNodes
[37.561735] Initial preNode count 613346
[37.564816] Destroyed 602327 preNodes
[37.564818] Concatenation over!
[37.564819] 565869 tips cut off
[37.564820] 11019 nodes left
[37.564908] Writing into pregraph file ./PreGraph...
[37.628994] Reading read set file ./Sequences;
[38.666026] 8855297 sequences found
[45.262765] Done
[47.287358] Reading pre-graph file ./PreGraph
[47.287449] Graph has 11019 nodes and 8855297 sequences
[47.320337] Scanning pre-graph file ./PreGraph for k-mers
[47.345965] 587492 kmers found
[47.410094] Sorting kmer occurence table ...
[47.807351] Sorting done.
[47.807356] Computing acceleration table...
[47.839961] Computing offsets...
[47.856571] Ghost Threading through reads 0 / 8855297
[49.327252] Ghost Threading through reads 100 / 8855297
[50.789941] Ghost Threading through reads 200 / 8855297

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-06 Thread Rodolfo Aramayo 
You are very welcome
So...what happened??
Thanks

--R

On Tue, Aug 6, 2013 at 9:26 AM, Greg Von Kuster g...@bx.psu.edu wrote:
 Hello Rodolfo,

 The following issue is resolved in 10319:61de03c05cf6 - thank for reporting 
 this.

 Greg Von Kuster

 On Aug 5, 2013, at 3:50 PM, Rodolfo Aramayo raram...@tamu.edu wrote:


 I did and it worked well it installed Blast 2.2.26+

 However there are two problems:

 1. On the admin page Installed tool shed repository 'ncbi_blast_plus'
 The name, Version and Type display correct values. However the
 'Installation status' shows no text





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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-05 Thread Rodolfo Aramayo 
Dear Peter,

APOLOGIES for the delayed response

Please see below for details..

On Thu, Aug 1, 2013 at 8:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
 On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:

 I've seen that kind of error from NCBI BLAST+ before - do you
 know which of the BLAST tools was this, and what the query
 was?

 The repo was:
 repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus

 The query was:
 Output from velvetoptimiser
 /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser

 OK, so this was a nucleotide FASTA file from an assembly, right?

 Yes

 What were you searching with BLAST? e.g. BLASTN against NT,
 BLASTX against NR, etc.

 Search was blastn, task megablast of the assembly as query against an
 in-house made (and installed into galaxy) of a blastn database for
 Chromosomes 1 to 7 of Neurospora crassa
 Database was produced with:
 makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title
 Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index
 and installed into the blastdb.loc file as required

 Can you run this blastn search 'by hand' at the terminal?

Yes, yes and no

 Does that crash too?

No and I do not know

Please let me explain.
I have set up the user galaxy account such that it has access to a
directory called 'bioinfosoft' where all bioinformatics-related
software is installed, including Blast+
Galaxy has 'access' to this directory and there I have compiled Blast+ 2.2.28+
Now, when I installed Blast+ via the toolshed, the toolshed Blast+
package did download and install what I believe it was the 2.2.26+
version of Blast+?
If I recall correctly, I got an error message that went away while the
Blast+ package was being compiled by the toolshed
The errors I got running Blast did all occur when using that
particular version of Blast+ (2.2.26)
I then removed or uninstalled the packaged and tried to re-install
again, but, as I said, it hanged there forever, installing...
To my surprise when I re-run the jobs, they all worked well. This is,
Blast worked like a charm BUT it did because it is NOT using the Blast
packaged that was installed by the toolshed but the Blast package I
compiled myself (2.2.28+) (SEE LOG AT END OF THIS MESSAGE...)

Comparing the directory of galaxy with those of my backups I can see
that the packaged Blast 2.2.26+ that was installed by the toolshed in
the directory:

./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/

is no longer there..

The directory:

./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/

is present but it is empty

Therefore to answer your questions:

 Can you run this blastn search 'by hand' at the terminal?

Yes, I can but I would be using a different version of Blast+

 Does that crash too?

No, because I would be using a different version of Blast+


 The error sounds very similar to this report which turned out
 to be due to a corrupted BLAST database - so also try
 recreating your DB:
 http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962

Regarding this last comment..basically a corrupt database is not the
problem in this case as demonstrated by the fact that I can run Blast
on those databases

Having said that, yes I have observed that depending on how one runs
the makeblastdb command and depending on the type of fasta files used,
you can end up with corrupt output. Some identifiers and symbols
present in the fasta ID can interfere with makeblastdb (especially
some produced by the JGI)

In summary, yes Blast+ is working but because is not using the
compiled Blast+ binaries installed by the toolshed package

The problem I have is that I would like to be able to properly
uninstall and re-install the Blast+ toolsheed so that things work as
they were originally supossed to

On the other hand, if you guys upgrade the package, this might be a
non-issue as the toolshed would just simply generate new directories...

Last, I noticed the command used in the compilation is different from
the one I normally use

The command I use is:

tar -xzvf ncbi-blast-2.2.28+-src.tar.gz
cd ncbi-blast-2.2.28+-src/c++
./configure --prefix=/usr/local/galaxy/bioinfosoft/blast-2.2.28+
--with-64 --with-bincopy --with-mt --without-debug --with-static | tee
c.log
make | tee m.log
make check
make install

Many Thanks


--Rodolfo


 Peter

LOG:

galaxy.jobs.handler INFO 2013-08-05 12:11:30,841 (2405) Job dispatched

galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell
command for dependency 'blastn'

galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve
dependency on 'blastn', ignoring

galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell
command for dependency 'blast+'

galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve
dependency on 'blast+', ignoring

galaxy.jobs.runners.local DEBUG 2013-08-05

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-05 Thread Rodolfo Aramayo 
Dave,

Also, when I click on:

Get repository update

I get the following error:
##
URL: 
http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
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 221 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 202 in check_for_updates
  repository = suc.get_installed_tool_shed_repository( trans, repository_id )
File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
line 515 in get_installed_tool_shed_repository
  return trans.sa_session.query( trans.model.ToolShedRepository ).get(
trans.security.decode_id( id ) )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
line 60 in decode_id
  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) )
ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'

##

Thanks

--R

On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier d...@bx.psu.edu wrote:
 Rodolfo,

 In order to simplify tracking down this issue, could you provide the
 changeset revision of Galaxy that is running on tamu.edu? To retrieve the
 revision, execute the following command in your galaxy root directory:

 hg id

 To clarify, our understanding is that you installed the ncbi_blast_plus
 repository from the main tool shed, and it installed correctly. You then
 uninstalled the repository, and it also uninstalled properly. You then
 attempted to reinstall the repository, and encountered the error message
 cited in your email.

 Can you confirm the above?

 We further understand that the repository is stuck in the 'installing'
 state. What options are available from the popup menu next to the
 ncbi_blast_plus repository on the manage installed repositories page? If
 'Deactivate or uninstall' is available, can you try uninstalling again, and
 see if that functions correctly?

--Dave B.


 On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:

 People,

 I successfully installed NCBI_Blast_Plus from the toolshed
 The tool, however, failed to work giving the following error:

 Fatal error: Exit code 255 ()
 Error: NCBI C++ Exception:

 /usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
 line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
 Attempt to access NULL pointer.

 I then tried uninstalling/reinstalling the tool

 However I now get an eternal 'installing' grey message and when I
 click 'manage the repo' I get:

 #

 URL:
 http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
 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 221 in decorator
return func( self, trans, *args, **kwargs )
 File
 '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 561 in manage_repository
repository = suc.get_installed_tool_shed_repository( trans,
 repository_id )
 File
 '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
 line 515 in get_installed_tool_shed_repository
return trans.sa_session.query( trans.model.ToolShedRepository ).get(
 trans.security.decode_id( id ) )
 File

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-05 Thread Rodolfo Aramayo 
Greg,

Please see my previous responses to Dave
I believe there are issues with the Tool Shed itself

Thanks

--R

On Mon, Aug 5, 2013 at 1:42 PM, Greg Von Kuster g...@bx.psu.edu wrote:
 The statement there are still issues with the Tool Shed itself is not
 confirmed, correct?  I believe we're still waiting on the response to Dave's
 initial response below.  Or did I miss it???

 On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier d...@bx.psu.edu wrote:

 Rodolfo,

 In order to simplify tracking down this issue, could you provide the
 changeset revision of Galaxy that is running on tamu.edu? To retrieve the
 revision, execute the following command in your galaxy root directory:

 hg id

 To clarify, our understanding is that you installed the ncbi_blast_plus
 repository from the main tool shed, and it installed correctly. You then
 uninstalled the repository, and it also uninstalled properly. You then
 attempted to reinstall the repository, and encountered the error message
 cited in your email.

 Can you confirm the above?

 We further understand that the repository is stuck in the 'installing'
 state. What options are available from the popup menu next to the
 ncbi_blast_plus repository on the manage installed repositories page? If
 'Deactivate or uninstall' is available, can you try uninstalling again, and
 see if that functions correctly?

   --Dave B.



 On Aug 5, 2013, at 2:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

 On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo raram...@tamu.edu wrote:

 Dear Peter,

 APOLOGIES for the delayed response

 Please see below for details..


 OK, so there are still issues with the Tool Shed itself,
 but the BLAST issue seems to have gone away when
 using a newer version (compiled). I'm working on using
 the NCBI provided binaries if possible, but updating
 the Galaxy BLAST+ bundle to a newer version of
 the underlying BLAST tools is planned.

 Thanks,

 Peter
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-05 Thread Rodolfo Aramayo 
Dave,

See below

On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier d...@bx.psu.edu wrote:
 Rodolfo,

 Please keep the thread on the mailing list by using the Reply all option.

Apologies


 You should now be able to go to the manage repository page, select the tool
 dependency, then select 'Manage tool dependencies' from the repository
 actions dropdown and reinstall the blast+ tool dependency.

--Dave B.


I did and it worked well it installed Blast 2.2.26+

However there are two problems:

1. On the admin page Installed tool shed repository 'ncbi_blast_plus'
The name, Version and Type display correct values. However the
'Installation status' shows no text

2. When I run the same blast job I was able to run before (using
Blast+ 2.2.28+...that I installed) I get the following:

error
An error occurred with this dataset: blastn: 2.2.26+ Package: blast
2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error:
NCBI C++ Exception:
/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
line 689: Critical:


Obviously it is the installed Blast that is at fault in here

Thanks

--R


 On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:

 Dear Dave,

 Answers below...

 On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier d...@bx.psu.edu wrote:

 Rodolfo,

 In order to simplify tracking down this issue, could you provide the
 changeset revision of Galaxy that is running on tamu.edu? To retrieve the
 revision, execute the following command in your galaxy root directory:

 hg id


 fd4113962c32+ (stable)


 To clarify, our understanding is that you installed the ncbi_blast_plus
 repository from the main tool shed, and it installed correctly. You then
 uninstalled the repository, and it also uninstalled properly. You then
 attempted to reinstall the repository, and encountered the error message
 cited in your email.

 Can you confirm the above?


 This is correct


 We further understand that the repository is stuck in the 'installing'
 state.


 YES and in the Manage installed tool shed repositories says now
 (after having to restart Galaxy for another reason):

 Installed, Missing tool dependencies


 What options are available from the popup menu next to the

 ncbi_blast_plus repository on the manage installed repositories page?


   If I click on the little arrow, it says:

 Get updates
 Deactivate or uninstall

 'Deactivate or uninstall' is available, can you try uninstalling again,
 and
 see if that functions correctly?


 It worked!

 Before I was not able to do it as I was getting an ugly galaxy error page
 But now it did uninstall and removed and was able to clone correctly.
 However, the directory:


 ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/

 is empty!


 Should I repopulate it with the one I have in my backup??

 Thanks

 --Rodolfo



 --Dave B.


 On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:


 People,

 I successfully installed NCBI_Blast_Plus from the toolshed
 The tool, however, failed to work giving the following error:

 Fatal error: Exit code 255 ()
 Error: NCBI C++ Exception:


 /usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
 line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
 Attempt to access NULL pointer.

 I then tried uninstalling/reinstalling the tool

 However I now get an eternal 'installing' grey message and when I
 click 'manage the repo' I get:

 #

 URL:

 http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
 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 221 in decorator
 return func( self, trans, *args, **kwargs )
 File

 '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 561 in manage_repository
 repository = suc.get_installed_tool_shed_repository( trans,
 repository_id )
 File
 '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
 line 515 in get_installed_tool_shed_repository
 return trans.sa_session.query( trans.model.ToolShedRepository ).get

[galaxy-dev] Galaxy cannot start last [server:handlerxx]

2013-08-05 Thread Rodolfo Aramayo 
Hi,

I have a 80 core/1TB RAM Dell server.
In order improve Galaxy performance I modified the universe_wsgi.ini
file so as to improve the Scaling and Load Balancing
as follows:

# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True

# Number of threads in the web server thread pool.
threadpool_workers = 200


[server:web0]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web1]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web2]
use = egg:Paste#http
port = 8092
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web3]
use = egg:Paste#http
port = 8093
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web4]
use = egg:Paste#http
port = 8094
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web5]
use = egg:Paste#http
port = 8095
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web6]
use = egg:Paste#http
port = 8096
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web7]
use = egg:Paste#http
port = 8097
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web8]
use = egg:Paste#http
port = 8098
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web9]
use = egg:Paste#http
port = 8099
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web10]
use = egg:Paste#http
port = 8100
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10


[server:manager]
use = egg:Paste#http
port = 8200
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5


[server:handler0]
use = egg:Paste#http
port = 8300
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler1]
use = egg:Paste#http
port = 8301
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler2]
use = egg:Paste#http
port = 8302
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler3]
use = egg:Paste#http
port = 8303
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler4]
use = egg:Paste#http
port = 8304
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler5]
use = egg:Paste#http
port = 8305
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler6]
use = egg:Paste#http
port = 8306
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler7]
use = egg:Paste#http
port = 8307
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler8]
use = egg:Paste#http
port = 8308
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler9]
use = egg:Paste#http
port = 8309
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler10]
use = egg:Paste#http
port = 8310
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler11]
use = egg:Paste#http
port = 8311
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler12]
use = egg:Paste#http
port = 8312
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler13]
use = egg:Paste#http
port = 8313
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler14]
use = egg:Paste#http
port = 8314
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler15]
use = egg:Paste#http
port = 8315
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler16]
use = egg:Paste#http
port = 8316
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler17]
use = egg:Paste#http
port = 8317
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler18]
use = egg:Paste#http
port = 8318
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

# [server:handler19]
# use = egg:Paste#http
# port = 8319
# host = 127.0.0.1
# use_threadpool = true
# threadpool_workers = 5

# [server:handler20]
# use = egg:Paste#http
# port = 8320
# host = 127.0.0.1
# use_threadpool = true
# threadpool_workers = 5


job_manager = manager
job_handlers = 
handler0,handler1,,handler2,handler3,handler4,handler5,handler6,handler7,handler8,handler9,handler10,handler11,handler12,handler13,handler14,handler15,handler16,handler17,handler18



Now the problem I have is that when I start galaxy I cannot get the
last [server:handler18] to load correclt
I get the following error:

galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,236 Enabling
'library_contents' API controller, class:

[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-01 Thread Rodolfo Aramayo 
People,

I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:

Fatal error: Exit code 255 ()
Error: NCBI C++ Exception:

/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
Attempt to access NULL pointer.

I then tried uninstalling/reinstalling the tool

However I now get an eternal 'installing' grey message and when I
click 'manage the repo' I get:

#

URL: 
http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
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 221 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 561 in manage_repository
  repository = suc.get_installed_tool_shed_repository( trans, repository_id )
File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
line 515 in get_installed_tool_shed_repository
  return trans.sa_session.query( trans.model.ToolShedRepository ).get(
trans.security.decode_id( id ) )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
line 60 in decode_id
  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) )
ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'

#

How can I totally uninstall and re-install this tool?

Thanks
___
Please keep all replies on the list by using reply all
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[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-01 Thread Rodolfo Aramayo 
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
 People,

 I successfully installed NCBI_Blast_Plus from the toolshed
 The tool, however, failed to work giving the following error:

 Fatal error: Exit code 255 ()
 Error: NCBI C++ Exception:
 
 /usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
 line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
 Attempt to access NULL pointer.

 I've seen that kind of error from NCBI BLAST+ before - do you
 know which of the BLAST tools was this, and what the query
 was?

The repo was:
repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus

The query was:
Output from velvetoptimiser
/repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser


 I then tried uninstalling/reinstalling the tool


 I doubt that will make any difference at all - this null pointer
 exception is not a problem from Galaxy.

 However I now get an eternal 'installing' grey message and when I
 click 'manage the repo' I get:

 #

 URL: 
 http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
 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 221 in decorator
   return func( self, trans, *args, **kwargs )
 File 
 '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 561 in manage_repository
   repository = suc.get_installed_tool_shed_repository( trans, repository_id )
 File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
 line 515 in get_installed_tool_shed_repository
   return trans.sa_session.query( trans.model.ToolShedRepository ).get(
 trans.security.decode_id( id ) )
 File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
 line 60 in decode_id
   return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! ) 
 )
 ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'

 #

 How can I totally uninstall and re-install this tool?

 Thanks

 You seem to have found a bug in the Tool Shed, so thank you
 for reporting this.

You are welcome

But any ideas on how to properly uninstall and re-install the tool??

Thanks

--R

 Peter
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[galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

2013-08-01 Thread Rodolfo Aramayo 
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
 On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
 On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
 People,

 I successfully installed NCBI_Blast_Plus from the toolshed
 The tool, however, failed to work giving the following error:

 Fatal error: Exit code 255 ()
 Error: NCBI C++ Exception:
 
 /usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp,
 line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
 Attempt to access NULL pointer.

 I've seen that kind of error from NCBI BLAST+ before - do you
 know which of the BLAST tools was this, and what the query
 was?

 The repo was:
 repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus

 The query was:
 Output from velvetoptimiser
 /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser

 OK, so this was a nucleotide FASTA file from an assembly, right?

Yes

 What were you searching with BLAST? e.g. BLASTN against NT,
 BLASTX against NR, etc.

Search was blastn, task megablast of the assembly as query against an
in-house made (and installed into galaxy) of a blastn database for
Chromosomes 1 to 7 of Neurospora crassa
Database was produced with:
makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title
Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index
and installed into the blastdb.loc file as required

Thanks



 How can I totally uninstall and re-install this tool?

 Thanks

 You seem to have found a bug in the Tool Shed, so thank you
 for reporting this.

 You are welcome

 But any ideas on how to properly uninstall and re-install the tool??


 Hopefully Greg from the Galaxy team will be able to help with this.

 Peter
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[galaxy-dev] The requested URL /cgi-bin-root/hgTracks was not found on this server

2013-06-17 Thread Rodolfo Aramayo 
Hi,

I starting getting this error since late galaxy update
I get  data from UCSC Main (local), but when I click display at UCSC main
I get:

Not Found
The requested URL /cgi-bin-root/hgTracks was not found on this server.

Please help

Thanks

--R
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[galaxy-dev] Making Public a Data Library Gives Internal Server Error

2013-05-30 Thread Rodolfo Aramayo 
Hi,

As Admin, I uploaded a set of files from filesystems paths
Uploading is successful but when I try to make the datasets public I get
the following error:

Internal Server Error

Galaxy was unable to sucessfully complete your request  ==By The
Way...NOTE how sucessfully is misspelled!!

URL:
http://galaxy.tamu.edu/library_common/make_library_item_public?library_id=8115c1ef1d2e7998show_deleted=Falseitem_type=lddacntrller=library_adminuse_panels=Falseid=a29602c45f6f1217
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
128 in __call__
  return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
184 in handle_request
  body = method( trans, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/library_common.py',
line 1626 in make_library_item_public
  self._check_access( trans, cntrller, is_admin, ldda.library_dataset,
current_user_roles, use_panels, library_id, show_deleted )
AttributeError: 'NoneType' object has no attribute 'library_dataset'

Help will be appreciated

Thanks


--R
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[galaxy-dev] Problems with rsync from datacache.g2.bx.psu.edu/indexes

2013-02-15 Thread Rodolfo Aramayo 
Hi,

I hope this is the right place to ask,

I am trying to rsync from:

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

and I am getting the error:

@ERROR: chroot failed
rsync error: error starting client-server protocol (code 5) at main.c(1534)
[Receiver=3.0.9

I know I can rsync to any other places

Do you happen to know what is going on?

Thanks

--Rodolfo
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[galaxy-dev] Backup_strategies_for_Galaxy

2012-08-20 Thread Rodolfo Aramayo 
Hi,

We are in the process of deploying a small Galaxy server here at Texas
AM University
I am a GNU/Linux kind of guy
My IT people want to use an SMB-mounted drive share as a backup destination
I am concerned that this might impact the performance of the server as
in my mind the equation is as follows:
SMB=Microsoft=windows=not_GNU/Linux=bad_Idea

But then again I am a geneticist

Any comments and/or other ideas??

Thanks

--Rodolfo
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