[galaxy-dev] Tophat issue

2012-12-27 Thread Luciano Cosme 
Howdy,
   I am getting the following error with tophat:

Error in tophat:

[2012-12-27 15:08:40] Beginning TopHat run (v2.0.5)
---
[2012-12-27 15:08:40] Checking for Bowtie
Traceback (most recent call last):
  File "/usr/bin/tophat", line 4035, in 
sys.exit(main())
  File "/usr/bin/tophat", line 3836, in main
check_bowtie(params)
  File "/usr/bin/tophat", line 1473, in check_bowtie
bowtie_version = get_bowtie_version(params.bowtie2)
  File "/usr/bin/tophat", line 1351, in get_bowtie_version
bowtie_version = [int(x) for x in ver_numbers[:3]] +
[int(ver_numbers[3][4:])]
IndexError: list index out of range

   I tried Tophat and Tophat2 a couple times and always giving me the same
error. The reads I am trying to map are from small RNA sequencing project.
I am trying to map the unannotated reads back to the genome. I am not sure
what is causing this problem, any help will be appreciated.

Thank you.

Luciano
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Re: [galaxy-dev] help configuring tools in Galaxy

2012-12-18 Thread Luciano Cosme 
Hi Tilahun,
   What you can do is to download the tools and make symlinks to /usr/bin.
You can download bowtie (http://bowtie-bio.sourceforge.net/manual.shtml),
tophat (http://tophat.cbcb.umd.edu/) and cufflinks (
http://cufflinks.cbcb.umd.edu/). Then after decompressing it, enter your
terminal and enter make the symlinks. For example, for one of the bowtie
files

sudo ln -s
/home/path-to-the-directory-where-you-put-all-files/bowtie/bowtie
/usr/bin/bowtie

   You have to create links to all executable files. You can make it in a
text editor and simply copy in the terminal. Not sure if that the easiest
way, but it works. If you get some permissions errors, you can change the
permissions of the files you are making symlinks to.
Best,


Luciano


On Tue, Dec 18, 2012 at 10:55 AM, Dannon Baker  wrote:

> Yep, that's the primary issue with tophat not being found -- you'll need
> to install binaries for some tools and potentially some reference genomes.
>
> See the wiki page here for lots more information:
> http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
>
>
> On Dec 18, 2012, at 11:48 AM, Tilahun Abebe  wrote:
>
> > Hi Dannon,
> >
> > I tried to run Bowtie2 and Tophat using a reference from history and
> these are the errors I got:
> >
> > An error occurred running this job: Error indexing reference sequence
> /bin/sh: bowtie2-build: command not found.
> >
> >
> > An error occurred running this job: Could not determine Tophat version
> /bin/sh: tophat: command not found Error indexing reference sequence
> /bin/sh: bowtie-build: command not found cp:
> /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/65/tophat_out/insertions.b
> >
> > I also tried to run eXpress on data mapped using Bowtie and this error
> came:
> >
> > An error occurred running this job: /bin/sh: express: command not found
> cp:
> /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/params.xprs:
> No such file or directory cp:
> /Users/abebe/tabix-0.2.6/python/galaxy-dist/database/job_working_directory/000/63/results.
> >
> > External dependencies might be the problem. We didn't do anything to
> install NGS tools or others for that matter. How do we install dependencies?
> >
> >
> > Thanks for your help.
> >
> > Tilahun
> > --
> >
> > On Tue, Dec 18, 2012 at 10:32 AM, Dannon Baker 
> wrote:
> > What specific errors are you seeing?  Some tools have external
> dependencies that need to be installed.
> >
> > -Dannon
> >
> > On Dec 18, 2012, at 11:29 AM, Tilahun Abebe 
> wrote:
> >
> > > Hi,
> > >
> > > We installed a local galaxy a couple of days ago following the basic
> installation instruction (http://wiki.galaxyproject.org/Admin/Get%20Galaxy).
> The installation went well, all the tools are listed on the left. I can
> also upload data to Galaxy. However, an error occurs when I try to run
> RNA-seq analysis. I am thinking the tools are not configured properly. Can
> you give me tips to configure NGS tools? An example file with setup syntax
> will help as well.
> > >
> > > Thanks.
> > >
> > > Tilahun
> > > ___
> > > 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/
> >
> >
>
> ___
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[galaxy-dev] Error while uploading data from local directory

2012-10-27 Thread Luciano Cosme 
Howdy,
   I installed galaxy in a new server that I build and I am getting the
following error when I try to upload the files from a local directory.

Error attempting to display contents of library (A.aegypti_mRNA):
(OperationalError) no such column: True u'SELECT dataset_permissions.id AS
dataset_permissions_id, dataset_permissions.create_time AS
dataset_permissions_create_time, dataset_permissions.update_time AS
dataset_permissions_update_time, dataset_permissions.action AS
dataset_permissions_action, dataset_permissions.dataset_id AS
dataset_permissions_dataset_id, dataset_permissions.role_id AS
dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND
dataset_permissions.action = ?' ['access'].

My raw data is stored in a different hard drive and I am just linking them
to Galaxy. I also changed the permissions recursively in the folder where
the data is (777). Any help will be appreciated.

Thank you.

Luciano



-- 
*Luciano Cosme*

-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
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Re: [galaxy-dev] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme 
Hi,
  I actually fixed it. I changed the wrapper in the line 105 from:
   cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file,
index_path )

to
   cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file,
index_path )

Luciano





On Tue, Jun 19, 2012 at 3:03 PM, Luciano Cosme wrote:

>
> Hi,
>I installed bowtie2 and when running tophat I get the following error:
>
> Error in tophat:
>
> [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
> ---
> [2012-06-19 14:02:39] Checking for Bowtie
> Bowtie version:2.0.0.6
> [2012-06-19 14:02:39] Checking for Samtools
>   Samtools version:0.1.18.0
> [2012-06-19 14:02:39] Checking for Bowtie index files
> Error: Could not find Bowtie 2 index files 
> (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)
>
>
>
> I was wondering if I can create the index files using bowtie2 via command
> line and then change the universe_wsgi.ini to:
>  # Temporary files are stored in this directory.
> new_file_path = database/tmp
>
>
> and put the index files there. Anyway, why is it not creating the indexes?
> I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
> then I get a error from tophat (bowtie not installed). Is it creating the
> index with bowtie 0.12.8?
> Thank you.
>
> Luciano
>



-- 
*Luciano Cosme*

-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
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[galaxy-dev] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme 
Hi,
   I installed bowtie2 and when running tophat I get the following error:

Error in tophat:

[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
---
[2012-06-19 14:02:39] Checking for Bowtie
  Bowtie version:2.0.0.6
[2012-06-19 14:02:39] Checking for Samtools
Samtools version:0.1.18.0
[2012-06-19 14:02:39] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
(/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)



I was wondering if I can create the index files using bowtie2 via command
line and then change the universe_wsgi.ini to:
 # Temporary files are stored in this directory.
new_file_path = database/tmp


and put the index files there. Anyway, why is it not creating the indexes?
I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
then I get a error from tophat (bowtie not installed). Is it creating the
index with bowtie 0.12.8?
Thank you.

Luciano
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Re: [galaxy-dev] Fwd: Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs

2012-05-22 Thread Luciano Cosme 
Hi,
  # /tmp was on /dev/sdb1 during installation
UUID=a2caec47-a863-42ee-a913-81b6596eeb14 /tmpext3
defaults0   2


# swap was on /dev/sda5 during installation
UUID=5bc28efd-40a3-4ea7-b391-24876e458d77 noneswap
sw  0   0

I created this line in fstab:

tmpfs /tmp tmpfs nodev,nosuid,size=100G  0 0



Thank you.

Luciano


On Mon, May 21, 2012 at 4:48 PM, Redmond, James  wrote:

>  Hi Luciano,
>
> ** **
>
> Just curious, but could you post the /tmp and swap lines from your fstab?
> I think I see your problem, but I’m not certain. Thanks!
>
> ** **
>
> Jim Redmond
>
> Department of Developmental Biology
>
> Washington University in St. Louis
>
> Office: +1-314-747-4033
>
> jredm...@wustl.edu
>
> ** **
>
> ** **
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Luciano Cosme
> *Sent:* Monday, May 21, 2012 4:17 PM
> *To:* galaxy-dev@lists.bx.psu.edu
> *Subject:* [galaxy-dev] Fwd: Load Files in local instance Ubuntu 12.04
> LTS /tmp as /tmpfs
>
> ** **
>
> Hi,
>   Actually Galaxy is using tmpfs mounted on /tmp. I just uploaded a small
> file and a big file. The small file works fine, but the big file (~20GB)
> did not. The tmpfs started getting used and stopped at 2.2GB, then I got a
> error from Galaxy.
> Here is the df -h:
> Filesystem  Size  Used Avail Use% Mounted on
> /dev/sda2   817G  3.9G  771G   1% /
> udev 12G  4.0K   12G   1% /dev
> *tmpfs   101G  2.2G   94G   3% /tmp*
> tmpfs   4.8G  992K  4.8G   1% /run
> none5.0M 0  5.0M   0% /run/lock
> none 12G   76K   12G   1% /run/shm
> /dev/sdb2   2.6T  101G  2.4T   4% /home
> /dev/sdc1   1.9T  1.6T  301G  84% /media/My Book
> /dev/sdb1   101G  2.2G   94G   3% /tmp
>
>
> Then I tried it again and I got same error tmpfs had 4.2GB:
> Filesystem  Size  Used Avail Use% Mounted on
> /dev/sda2   817G  3.9G  771G   1% /
> udev 12G  4.0K   12G   1% /dev
> *tmpfs   101G  4.2G   92G   5% /tmp*
> tmpfs   4.8G  992K  4.8G   1% /run
> none5.0M 0  5.0M   0% /run/lock
> none 12G   76K   12G   1% /run/shm
> /dev/sdb2   2.6T  101G  2.4T   4% /home
> /dev/sdc1   1.9T  1.6T  301G  84% /media/My Book
> /dev/sdb1   101G  4.2G   92G   5% /tmp
>
> Here is the galaxy error:
> 
> Exception happened during processing of request from ('127.0.0.1', 33382)
> Traceback (most recent call last):
>   File
> "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 1053, in process_request_in_thread
> self.finish_request(request, client_address)
>   File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
> self.RequestHandlerClass(request, client_address, self)
>   File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
> self.handle()
>   File
> "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 432, in handle
> BaseHTTPRequestHandler.handle(self)
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
> self.handle_one_request()
>   File
> "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 427, in handle_one_request
> self.wsgi_execute()
>   File
> "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 287, in wsgi_execute
> self.wsgi_start_response)
>   File
> "/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
> line 202, in __call__
> return app(environ, start_response)
>   File
> "/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/xforwardedhost.py",
> line 21, in __call__
> return self.app( environ, start_response )
>   File
> "/home/koala2/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
> line 164, in __call__
> app_iter = self.application(environ, start_response)
>   File
> "/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/translogger.py",
> line 68, in __call__
> return self.application(environ, replacement_start_response)
>   File
> "/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
> line 226, in __call__
> return self.respond(environ, start_response)
>   File
> "/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
&g

[galaxy-dev] Fwd: Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs

2012-05-21 Thread Luciano Cosme 
Hi,
  Actually Galaxy is using tmpfs mounted on /tmp. I just uploaded a small
file and a big file. The small file works fine, but the big file (~20GB)
did not. The tmpfs started getting used and stopped at 2.2GB, then I got a
error from Galaxy.
Here is the df -h:
Filesystem  Size  Used Avail Use% Mounted on
/dev/sda2   817G  3.9G  771G   1% /
udev 12G  4.0K   12G   1% /dev
*tmpfs   101G  2.2G   94G   3% /tmp*
tmpfs   4.8G  992K  4.8G   1% /run
none5.0M 0  5.0M   0% /run/lock
none 12G   76K   12G   1% /run/shm
/dev/sdb2   2.6T  101G  2.4T   4% /home
/dev/sdc1   1.9T  1.6T  301G  84% /media/My Book
/dev/sdb1   101G  2.2G   94G   3% /tmp


Then I tried it again and I got same error tmpfs had 4.2GB:
Filesystem  Size  Used Avail Use% Mounted on
/dev/sda2   817G  3.9G  771G   1% /
udev 12G  4.0K   12G   1% /dev
*tmpfs   101G  4.2G   92G   5% /tmp*
tmpfs   4.8G  992K  4.8G   1% /run
none5.0M 0  5.0M   0% /run/lock
none 12G   76K   12G   1% /run/shm
/dev/sdb2   2.6T  101G  2.4T   4% /home
/dev/sdc1   1.9T  1.6T  301G  84% /media/My Book
/dev/sdb1   101G  4.2G   92G   5% /tmp

Here is the galaxy error:

Exception happened during processing of request from ('127.0.0.1', 33382)
Traceback (most recent call last):
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
self.handle()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
self.handle_one_request()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
  File
"/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
  File
"/home/koala2/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
  File
"/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
  File
"/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
  File
"/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 900, in params
params = self.str_params
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 818, in str_POST
keep_blank_values=True)
  File "/usr/lib/python2.7/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 510, in __init__
self.read_single()
  File "/usr/lib/python2.7/cgi.py", line 647, in read_single
self.read_lines()
  File "/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py", line
268, in read_lines
self.read_lines_to_outerboundary()
  File "/usr/lib/python2.7/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
  File "/usr/lib/python2.7/socket.py", line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is less than minimum


Thank you.

[galaxy-dev] Load Files in local instance Ubuntu 12.04 LTS /tmp as /tmpfs

2012-05-21 Thread Luciano Cosme 
Hi,
   I decided to format my PC and reinstall everything. I have Ubuntu
12.04LTS installed in one 1TB hard drive (/ and swap) and the /home folder
installed in a 3TB hard drive. I created a /tmp partition of 110GB and a
/tmp partion of 110GB, both in the 1TB HD. Then I mounted /tmp as /tmpfs
using fstab. Here is the df -h output:

Filesystem  Size  Used Avail Use% Mounted on
/dev/sda2   817G  3.9G  771G   1% /
udev 12G  4.0K   12G   1% /dev
tmpfs   100G   16K  100G   1% /tmp
tmpfs   4.8G  992K  4.8G   1% /run
none5.0M 0  5.0M   0% /run/lock
none 12G  148K   12G   1% /run/shm
/dev/sdb2   2.6T   99G  2.4T   4% /home
/dev/sdc1   1.9T  1.6T  301G  84% /media/My Book

  Then I try to upload files as administrator on my local instance of
galaxy and it fails. Since I even have a swap partition with 100GB and
using the /tmp partition I don't know why it is not working. What I notice
is that it is using the /tmpfs mounted on /run, which is only 4.8GB. I also
tried to change universe.ini to use /tmp as temporary files storage:
# Temporary files are stored in this directory.
new_file_path = /tmp

 I can upload files that are smaller than 4.8GB, but not bigger than it.
Previously it was working fine on the other Ubuntu version.  I was using
/tmp as tmpfs, but I don't know how to configure the Galaxy to use the the
tmpfs mounted at /tmp and not the tmpfs mounted at /run. I asked similar
question before and I was able to fix it on Ubuntu 10.04 LTS, but now
Ubuntu have this tmpfs mounted on /run, which is not in fstab.
   Thank you.

Luciano




-- 
*Luciano Cosme*

-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
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Re: [galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'

2012-05-14 Thread Luciano Cosme 
Hi,
  Yes. It is same user and the only used of this system.
Thank you.


On Fri, May 11, 2012 at 1:33 PM, Nate Coraor  wrote:

>
> On May 10, 2012, at 6:59 PM, Luciano Cosme wrote:
>
> >
> > Hi Everyone,
> >I was just using my local galaxy instance. I closed it up (from
> terminal), open IGV to look at some genes, then I restarted it from the
> terminal and when I tried to access it I got the error message below. I
> just don't know what happened in these few minutes. Any suggestion how to
> fix it?
> > Thank you.
> >
> > Luciano
> >
> > URL: http://127.0.0.1:8080/
> >
> ...
> >  module = imp.load_source(self.module_id, path, open(path, 'rb'))
> > IOError: [Errno 13] Permission denied:
> u'/home/koala2/galaxy-central/database/compiled_templates/
> base_panels.mako.py'
>
> Hi Luciano,
>
> Could you verify that you started Galaxy as the same user both times?
>
> --nate
>
> >
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[galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'

2012-05-10 Thread Luciano Cosme 
Hi Everyone,
   I was just using my local galaxy instance. I closed it up (from
terminal), open IGV to look at some genes, then I restarted it from the
terminal and when I tried to access it I got the error message below. I
just don't know what happened in these few minutes. Any suggestion how to
fix it?
Thank you.

Luciano

URL: http://127.0.0.1:8080/
File
'/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
  environ, self.app)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
  return self.application(environ, start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
  return self.application(environ, start_response)
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py', line
160 in __call__
  body = method( trans, **kwargs )
File '/home/koala2/galaxy-central/lib/galaxy/web/controllers/root.py', line
25 in index
  m_c=m_c, m_a=m_a )
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 733 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 744 in fill_template_mako
  return template.render( **data )
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 296 in render
  return runtime._render(self, self.callable_, args, data)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 660 in _render
  **_kwargs_for_callable(callable_, data))
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 691 in _render_context
  (inherit, lclcontext) = _populate_self_namespace(context, tmpl)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 637 in _populate_self_namespace
  ret = template.module._mako_inherit(template, context)
File '/home/koala2/galaxy-central/database/compiled_templates/root/
index.mako.py', line 25 in _mako_inherit
  return runtime._inherit_from(context,
u'/webapps/galaxy/base_panels.mako', _template_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 609 in _inherit_from
  ret = callable_(template, lclcontext)
File
'/home/koala2/galaxy-central/database/compiled_templates/webapps/galaxy/
base_panels.mako.py', line 25 in _mako_inherit
  return runtime._inherit_from(context, u'/base_panels.mako', _template_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 596 in _inherit_from
  template = _lookup_template(context, uri, calling_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 626 in _lookup_template
  return lookup.get_template(uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py',
line 218 in get_template
  return self._load(srcfile, uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py',
line 283 in _load
  **self.template_args)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 218 in __init__
  module = self._compile_from_file(path, filename)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 245 in _compile_from_file
  module = imp.load_source(self.module_id, path, open(path, 'rb'))
IOError: [Errno 13] Permission denied:
u'/home/koala2/galaxy-central/database/compiled_templates/
base_panels.mako.py'
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[galaxy-dev] Error while uploading

2012-03-10 Thread Luciano Cosme 
Hi,
   I uploaded 11 files today (1 to 2Gb compressed files) to my local
instance without a problem (as admin). Then I got this error message below
and it get stuck at "This dataset is uploading" and I could not upload the
last files. Is there anything I can do to solve it? What I notice is that I
can still upload small files, before I concatenate them. I have 15 time
points and some of them have up to 20 files, so it is easier to concatenate
them and them upload.
Thank you.

Luciano



127.0.0.1 - - [10/Mar/2012:17:01:47 -0500] "POST
/library_common/upload_library_dataset HTTP/1.1" 500 - "
http://127.0.0.1:8080/library_common/upload_library_dataset?library_id=f597429621d6eb2b&show_deleted=False&cntrller=library_admin&folder_id=f597429621d6eb2b&use_panels=False";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
Firefox/10.0.2"
Debug at: http://127.0.0.1:8080/_debug/view/1331420472

Exception happened during processing of request from ('127.0.0.1', 35033)
Traceback (most recent call last):
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 639, in __init__
self.handle()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 343, in handle
self.handle_one_request()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
  File
"/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
  File
"/home/koala2/galaxy-central/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
  File
"/home/koala2/galaxy-central/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
  File
"/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
  File
"/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 900, in params
params = self.str_params
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
  File
"/home/koala2/galaxy-central/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 818, in str_POST
keep_blank_values=True)
  File "/usr/lib/python2.7/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 510, in __init__
self.read_single()
  File "/usr/lib/python2.7/cgi.py", line 647, in read_single
self.read_lines()
  File "/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py", line
268, in read_lines
self.read_lines_to_outerboundary()
  File "/usr/lib/python2.7/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
  File
"/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
  File "/usr/lib/python2.7/socket.py", line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is less than minimum

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Re: [galaxy-dev] uploads stuck in history

2012-03-05 Thread Luciano Cosme 
Hi,
  I was trying to upload data again and here is the error message that I
get:

Can't create peek [Errno 2] No such file or directory:
'/home/koala2/galaxy-dist/database/files/000/dataset_24.dat'




Exception happened during processing of request from ('127.0.0.1', 52338)
Traceback (most recent call last):
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 639, in __init__
self.handle()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 432, in handle
BaseHTTPRequestHandler.handle(self)
  File "/usr/lib/python2.7/BaseHTTPServer.py", line 343, in handle
self.handle_one_request()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 427, in handle_one_request
self.wsgi_execute()
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 287, in wsgi_execute
self.wsgi_start_response)
  File "/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
line 202, in __call__
return app(environ, start_response)
  File
"/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
line 21, in __call__
return self.app( environ, start_response )
  File
"/home/koala2/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
line 164, in __call__
app_iter = self.application(environ, start_response)
  File
"/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
line 68, in __call__
return self.application(environ, replacement_start_response)
  File
"/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 226, in __call__
return self.respond(environ, start_response)
  File
"/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
line 399, in respond
if self.xmlhttp_key in req.params:
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 900, in params
params = self.str_params
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
  File
"/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py",
line 818, in str_POST
keep_blank_values=True)
  File "/usr/lib/python2.7/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
  File "/usr/lib/python2.7/cgi.py", line 510, in __init__
self.read_single()
  File "/usr/lib/python2.7/cgi.py", line 647, in read_single
self.read_lines()
  File "/home/koala2/galaxy-dist/lib/galaxy/web/framework/base.py", line
268, in read_lines
self.read_lines_to_outerboundary()
  File "/usr/lib/python2.7/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
  File
"/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
line 467, in readline
data = self.file.readline(self.length - self._consumed)
  File "/usr/lib/python2.7/socket.py", line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is greater than maximum



On Mon, Mar 5, 2012 at 3:24 PM, Luciano Cosme wrote:

> I had same issue recently. I tried to upload files locally and give same
> error (from 50Mb or 17Gb as admin). The files never finish uploading. A few
> days ago I tried to upload around 20 files (up to 200Mb), most of them
> uploaded normally, but some wouldn't. I will try a different browser them
> Thanks.
>
>
>
> > 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu
> HTTP/1.1" 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux
> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>
>
>
>
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Re: [galaxy-dev] uploads stuck in history

2012-03-05 Thread Luciano Cosme 
I had same issue recently. I tried to upload files locally and give same
error (from 50Mb or 17Gb as admin). The files never finish uploading. A few
days ago I tried to upload around 20 files (up to 200Mb), most of them
uploaded normally, but some wouldn't. I will try a different browser them
Thanks.


> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1"
200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"


Luciano
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Re: [galaxy-dev] [galaxy-user] about ftp setting up

2011-12-19 Thread Luciano Cosme 

Hi Liao,
   I had similar problem with the postgresql whiling setting up my  
ftp server. The easy way to upload files to your local instance of  
Galaxy is to setup an admin user. You can find the instructions how to  
do it here http://wiki.g2.bx.psu.edu/Admin/Interface Now you can  
upload files really fast.


Luciano

On Dec 14, 2011, at 1:28 AM, Liao_Ruiqi wrote:


Hello there，
   I'm a student at Fudan University in China. I was trying to  
enable ftp uploading in my local version of GALAXY.
I tried the setting in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP 
, but I got the following problems:
1. The galaxyftp seems to be a pasql database, shall I build it  
myself? or dose it already exists in galaxy directory?
2. the galaxy_user seems to be a table, shall I build it myself? and  
how shall I update it and integrate it with galaxy?


Thanks for your attention, and looking forward to your reply!

Best wishes

Liao Ruiqi


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-------
Luciano Cosme
PhD Candidate
Texas A&M Entomology
co...@tamu.edu
---






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Re: [galaxy-dev] file upload issue

2011-12-15 Thread Luciano Cosme 

Hi,
I am having the same issue today. It was working a few days ago,  
but now never finish uploading.


Luciano


On Dec 15, 2011, at 3:05 PM, weihong yan wrote:



I recently installed galaxy program on our Linux server and it is  
going to be used for analyzing high-throuput sequencing data.   I  
tried  to upload a dataset (a bed format file) from local computer  
to galaxy server, but no success.  The message of "Dataset is  
uploading" stays forever.  The uploaded dataset was shown on the / 
galaxy-dist/database/tmp directory, but it didn't get transferred to  
the job-working directory or files directory before it was deleted  
by the galaxy.


The output of run_functional_tests shows that uploading file went  
successfully.  The paster.log file doesn't show error message about  
the uploading.


Any configuration did I miss?   Your feedback is highly appreciated.

Thank you!


Weihong


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Re: [galaxy-dev] Database configuration

2011-10-21 Thread Luciano Cosme 
eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/schema.py",
line 236, in __init__
_bind_or_error(metadata).reflecttable(self,
include_columns=include_columns)
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
line 1261, in reflecttable
conn = self.contextual_connect()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py",
line 1229, in contextual_connect
return self.Connection(self, self.pool.connect(),
close_with_result=close_with_result, **kwargs)
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 142, in connect
return _ConnectionFairy(self).checkout()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 304, in __init__
rec = self._connection_record = pool.get()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 161, in get
return self.do_get()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 639, in do_get
con = self.create_connection()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 122, in create_connection
return _ConnectionRecord(self)
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 198, in __init__
self.connection = self.__connect()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/pool.py",
line 261, in __connect
connection = self.__pool._creator()
  File
"/home/koala2/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/strategies.py",
line 80, in connect
raise exc.DBAPIError.instance(None, None, e)
OperationalError: (OperationalError) could not connect to server: No such
file or directory
Is the server running locally and accepting
connections on Unix domain socket "/tmp/.s.PGSQL.5432"?
 None None

Turns out that my server is not starting too:

koala2@aedes:~$ sudo /etc/init.d/proftpd start
 * Starting ftp server proftpd
- Fatal: unknown configuration directive 'SQLPasswordEngine' on line 43 of
'/etc/proftpd/proftpd.conf' [fail]

I checked the the proftpd.conf that I prepared:

42 # Set up mod_sql_password - Galaxy passwords are stored as hex-encoded
SHA1
43 SQLPasswordEngine on
44 SQLPasswordEncoding hex

Any suggestion how to solve it. I was using the my local instance before,
but getting the files from Amazon s3 buckets, but that takes too long and I
am not using the cloud anymore.
Thank you.

Luciano















On Thu, Oct 20, 2011 at 6:59 PM, Greg Von Kuster  wrote:

> Luciano,
>
> You only need to create the database instance itself, you do not need to
> manually create any tables.  When you have created the database instance,
> configure the path to it using the database_connection setting in
> universe_wsgi.ini, something like:
>
> database_connection =
> postgres:///galaxy_dbt?user=postgres&password=postgres
>
> This is all you need to do.  Then start up the Galaxy server with:
>
> sh run.sh
>
> and Galaxy will automatically create all of the necessary tables for you.
>
> Greg Von Kuster
>
> On Oct 20, 2011, at 7:44 PM, Luciano Cosme wrote:
>
> Hi,
>I am sorry about the trivial questions. I am following this guide
> http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp
> server to upload data to my local instance of galaxy. I am getting a error
> when I am configuring the database server:
>
> postgres@aedes:~$ createuser -SDR galaxyftp
> postgres@aedes:~$ psql galaxydb
> psql (9.1.1)
> Type "help" for help.
>
> galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword';
> ALTER ROLE
> galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp;
> ERROR:  relation "galaxy_user" does not exist
> galaxydb=#
>
>
> It might be something pretty simple, but I am new to it and any help will
> be appreciated. I create the user galaxy_user already.
>
> Thank you.
> Luciano
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>
> Greg Von Kuster
> Galaxy Development Team
> g...@bx.psu.edu
>
>
>
>
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[galaxy-dev] Database configuration

2011-10-20 Thread Luciano Cosme 
Hi,
   I am sorry about the trivial questions. I am following this guide
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp
server to upload data to my local instance of galaxy. I am getting a error
when I am configuring the database server:

postgres@aedes:~$ createuser -SDR galaxyftp
postgres@aedes:~$ psql galaxydb
psql (9.1.1)
Type "help" for help.

galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword';
ALTER ROLE
galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp;
ERROR:  relation "galaxy_user" does not exist
galaxydb=#


It might be something pretty simple, but I am new to it and any help will be
appreciated. I create the user galaxy_user already.

Thank you.
Luciano
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[galaxy-dev] samtools question

2011-08-01 Thread Luciano Cosme 
Hi Everyone,
   I am running galaxy locally (ubuntu 11.04) and I am having problem with
samtools. When I am running TopHat I get an error message saying that could
not locate samtools. Of course I did everything described in
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
 Here is the error message:

Error in tophat:

[Mon Aug  1 13:03:53 2011] Beginning TopHat run (v1.3.1)
---
[Mon Aug  1 13:03:53 2011] Preparing output location ./tophat_out/
[Mon Aug  1 13:03:53 2011] Checking for Bowtie index files
[Mon Aug  1 13:03:53 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /tmp/tmpkcZN3L/dataset_26.dat.fa
[Mon Aug  1 13:03:53 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /bin/bowtie-inspect /tmp/tmpkcZN3L/dataset_26.dat >
./tophat_out/tmp/dataset_26.dat.fa
[Mon Aug  1 13:04:41 2011] Checking for Bowtie
Bowtie version:  0.12.7.0
[Mon Aug  1 13:04:42 2011] Checking for Samtools
Error locating program: samtools


When I run "make" in the samtools directory I also get an error message:

koala2@aedes:~/Desktop/galaxy/samtools$ make
make[1]: Entering directory `/home/koala2/Desktop/galaxy/samtools'
make[2]: Entering directory `/home/koala2/Desktop/galaxy/samtools'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1
-I. bgzf.c -o bgzf.o
In file included from bgzf.c:36:0:
bgzf.h:30:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/koala2/Desktop/galaxy/samtools'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/koala2/Desktop/galaxy/samtools'
make: *** [all-recur] Error 1

I also followed the installation guide from samtools, but did not work
either.

Unfortunately I found myself spending more time installing tools than using
it. Yes I am a newbie.
Thank you.

Luciano
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