[galaxy-dev] Local galaxy

2012-12-13 Thread Jennifer Jackson

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Hi
I am doing NGS analysis in our local galaxy, I would like to access the output 
files for further analysis.
I do have an account on the server where galaxy is installed, so I would like 
to access the output files without actually downloading them( aince they are 
huge). Can you please tell me where I can find my (local galaxy) output files 
on the server ? Is it stored under databases ?
Thanks.
Selvi Ramalingam

Sent from my iPhone

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http://galaxyproject.org

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Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

2012-12-13 Thread Jennifer Jackson

Hello Sachit,

There are a few problems with the command line. If you want to install 
hg19, then hg16 should not be used. Also, the reference_in to the tool 
should be an uncompressed fasta file. This is described in the tool 
documentation.


You will also need to use as the 'index_basename' the same dbkey 
identifier for the genome as you are using to name the reference fasta 
file (minus the .fasta extension) and for the SAM index. This is also 
the same dbkey identifier as used in the 
$GALAXYROOT/tool-data/shared/ucsc/builds.txt file. Using simply hg19 
as the dbkey would be the simplest choice.


The original link I sent you explains this, but perhaps you did not find 
the data integration wiki page linked from the top? It is important to 
know about, as it also covers the builds.txt file in the first section. 
It can be found here:

http://wiki.galaxyproject.org/Admin/Data%20Integration

You may find it helpful to rsync the current hg19 genome and indexes 
from our server to help you get started. These could be used as a base 
from where bowtie2 indexes could be added. Please note that some 
genomes, including hg19, have variants in our data archives and that 
this particular genome is very large with many indexes and related files 
(just a warning if space is a concern). The tool forms for the RNA-seq 
tools describe variant content, but in short, the full genome is the 
same as the original. It is important to follow the symbolic links to 
note which datasets are associated with which indexes and to follow the 
same conventions when adding new data. Or take what you need and 
reorganize is as it makes the most sense for your own use. This is not 
overly complicated - you will be able to see which are associated by 
browsing the contained data. The second section on the data integration 
wiki page above describes how to rsync, if you choose to do this.


To use the data, even rsync data, the loc files must still be set up. 
You only have to set up the ones that you plan to use. The original wiki 
link and the one above have information about .loc files, as do the 
sample .loc files themselves.


Hopefully this helps,

Jen
Galaxy team


On 12/12/12 9:56 PM, Sachit Adhikari wrote:

I need to install hg19 not hg16.

On Thu, Dec 13, 2012 at 4:26 AM, Sachit Adhikari 
sachit.techner...@gmail.com mailto:sachit.techner...@gmail.com wrote:


Hello Jen,

Thanks for your reply. I have installed bowtie2 and tophat2. I am
trying to use this command to build the index:
bowtie2-build [options]* reference_in index_basename

My file name is Homo_sapiens_UCSC_hg19.tar.gz. Thus I used
bowtie2-build -f Homo_sapiens_UCSC_hg19.tar.gz hg16

But it doesn't work. What am I doing wrong? Thanks

On Wed, Dec 12, 2012 at 9:23 PM, Jennifer Jackson j...@bx.psu.edu
mailto:j...@bx.psu.edu wrote:

Hello Sachit,

Instructions for setting up local indexes are in our wiki here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Bowtie2 is not specifically listed, but the instructions for
Bowtie and Bowtie2 are nearly identical. The same indexes are
used for Bowtie2 and Tophat2. When building the index, you
simply replace bowtie-build with bowtie2-build in the
command string and create/modify the bowtie2_index.loc file
the same as you would the bowtie_index.loc file.

The Tophat2 manual has some more details about getting set up
here:
http://tophat.cbcb.umd.edu/manual.html

Next time, for questions about local installs, using just the
galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu list is
best (no need to post to multiple lists). If your question has
been misunderstood, please send more details to clarify.

Best,

Jen
Galaxy team



On 12/12/12 3:46 AM, Sachit Adhikari wrote:

How do I add hg16 into the build-in index?


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Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Greg Von Kuster
Hi Lance,

What process did you use for updating the tool shed repository and how many 
separate repositories did you use?  You should not be updating a local 
repository, pushing the changes to the tool shed repository, and then 
attempting to pull the changes back to the same repository.  Your repository 
environment should be something like this:

DEV REPO ( all development updates are performed here, so this is where the 
tool version is incremented )
|
   V
pushed changeset
   |
   V
EXISTING TOOL SHED REPO
   |
  V
pulled changeset to some previously cloned repo
   |
  V
PREVIOUSLY CLONED (possibly production) REPO

In other words, nothing should ever get pushed and pulled from the tool shed 
repo into the same repo.  If this is the process you used, it would undoubtedly 
result in the behavior you saw.  If you used separate repos as I describe 
above, we'll need more details as to the process you used in order to determine 
the cause of the problem.

Greg Von Kuster


On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:

 I recently updated the htseq-count tool in the Galaxy toolshed to version 
 0.3.  This version has some functional changes and thus the tool version was 
 incremented.  I installed this new version of the tool in my local Galaxy 
 instance.
 
 However, I realized later that I missed updating one part of the help text. 
 Today I fixed that text (but left the tool version the same), tarred up the 
 file, and uploaded it to the toolshed.  I then attempted to Get Updates 
 from my local Galaxy instances for that tool got the following error:
 
 URL: 
 http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/name=htseq_countowner=lparsonschangeset_revision=5d969cb56112latest_changeset_revision=f320093f1e8elatest_ctx_rev=11
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
  line 364 in respond
 app_iter = self.application(environ, detect_start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', 
 line 98 in __call__
 environ, self.app)
 File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 
 line 539 in intercept_output
 app_iter = application(environ, replacement_start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
 line 80 in __call__
 return self.application(environ, start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
  line 91 in __call__
 return self.app( environ, start_response )
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
  line 632 in __call__
 return self.application(environ, start_response)
 File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 
 in __call__
 body = method( trans, **kwargs )
 File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 
 206 in decorator
 return func( self, trans, *args, **kwargs )
 File 
 '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1677 in update_to_changeset_revision
 update_repository( repo, latest_ctx_rev )
 File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', line 
 1428 in update_repository
 rev=ctx_rev )
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
  line 5661 in update
 rev = scmutil.revsingle(repo, rev, rev).rev()
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
  line 515 in revsingle
 l = revrange(repo, [revspec])
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
  line 588 in revrange
 for r in m(repo, range(len(repo))):
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
  line 1414 in mfunc
 return getset(repo, subset, tree)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
  line 156 in getset
 return methods[x[0]](repo, subset, *x[1:])
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
  line 171 in symbolset
 return stringset(repo, subset, x)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py',
  line 161 in stringset
 x = repo[x].rev()
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py',
  line 235 in __getitem__
 return context.changectx(self, changeid)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py',
  line 103 in __init__
 _(unknown revision '%s') % changeid)
 RepoLookupError: unknown revision '11'
 
 
 I believe this is because the revision I have installed (10) is not 

Re: [galaxy-dev] Local galaxy

2012-12-13 Thread Jeremy Goecks
 
 
 
 Hi
 I am doing NGS analysis in our local galaxy, I would like to access the 
 output files for further analysis.
 I do have an account on the server where galaxy is installed, so I would like 
 to access the output files without actually downloading them( aince they are 
 huge). Can you please tell me where I can find my (local galaxy) output files 
 on the server ? Is it stored under databases ?

Take a look at the following settings in your universe_wsgi.ini file:

file_path - where datasets are stored
expose_dataset_path - allows admins/users to see a dataset's path in the 
dataset information panel

Best,
J.
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Re: [galaxy-dev] Custom Builds Server eroor

2012-12-13 Thread Hans-Rudolf Hotz

Hi Shaun

I recently run into troubles creating a visualization for a custom build 
using a fasta file to provide the sequence lengths.


In order to continue, I had to remove the entry from the database, ie: 
changing the value to {} for name = 'dbkeys' in the 'user_preference' 
table.



I repeated it by adding the sequence length manually and it worked. I 
then run into the next problem: I couldn't add new wiggle or bed files 
to a data library using this custom build. However, once in the data 
library I could change the genome to the custom one.



Regards, Hans-Rudolf





On 12/12/2012 08:09 PM, Jeremy Goecks wrote:



Hello I added a custom build to Galaxy, then deleted it and added a new build 
with the same name. Now whenever I try to acces my custom builds I am getting a 
server error.


I can't reproduce this issue using the most recent galaxy-dist. Also, the stack 
trace that you pasted below doesn't relate to custom builds; it relates to 
visualizing the data with Ensembl.

Can you be more specific about what steps you took and what your goal is?

Thanks,
J.


Can you point me towards any faults? Do I need to manually remove the custom 
builds from the database and if so where can I find them?

Thanks
Shaun Webb


Error - type 'exceptions.KeyError': u'ensembl_Current'
URL: 
http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f6e2/ensembl_interval/ensembl_Current
File 
'/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
 line 143 in __call__
  app_iter = self.application(environ, start_response)
File 
'/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
 line 80 in __call__
  return self.application(environ, start_response)
File 
'/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
 line 632 in __call__
  return self.application(environ, start_response)
File 
'/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', 
line 160 in __call__
  body = method( trans, **kwargs )
File 
'/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
 line 740 in display_application
  display_link = display_app.get_link( link_name, data, dataset_hash, 
user_hash, trans )
File 
'/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py',
 line 189 in get_link
  return PopulatedDisplayApplicationLink( self.links[ link_name ], data, 
dataset_hash, user_hash, trans )
File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in 
__getitem__
  raise KeyError(key)
KeyError: u'ensembl_Current'







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[galaxy-dev] hg pull aborted

2012-12-13 Thread Sarah Maman

Hello,

When updating local instance of our Galaxy, the hg aborted:
pulling from https://bitbucket.org/galaxy/galaxy-dist/
searching for changes
adding changesets
adding manifests
adding file changes
added 1482 changesets with 3989 changes to 1340 files
abort: untracked file in working directory differs from file in 
requested revision: 'doc/Makefile'


and :
-bash-3.2$ hg update
abort: untracked file in working directory differs from file in 
requested revision: 'doc/source/conf.py'




Could you please tell me what this may be the problem?

Thanks
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[galaxy-dev] Fw: Questions about Install GATK on local instance

2012-12-13 Thread ygong
Hi,

Could anyone give me some suggestions about that?
Thanks very much.

Anthonel

- Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM -

From:   Yixiao Gong/cpdr/hjf
To: galaxy-dev@lists.bx.psu.edu
Date:   12/12/2012 02:52 PM
Subject:Questions about Install GATK on local instance


Hi, all,

I'm installing GATK on galaxy local instance now and I have some questions 
may need your help.

I downloaded the GATK2 from GATK website htt 
http://www.broadinstitute.org/gatk/download  . the link is 
http://www.broadinstitute.org/gatk/auth?package=GATK

I knew that on galaxy tool dependencies page 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave 
the link for GATK 1.4 version but I can't figure out how to download and 
install it, and I noticed that GATK2 have all 1.x version features, so I 
installed GATK2. 

In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are 
multiple folders and files and I got really confused what I need to 
download. Even I choose ZIP to download a zip file, I counld not figure 
out whether it is the program package and don't know how to install it.

Maybe this is the problem. But based on my understanding, GATK is just a 
set of java package, and all we need to do is put it into 
/tool-data/shared/jars folder, right? That is how I did it for GATK2. The 
GATK2 package include a folder called resources and a file called 
GenomeAnalysisTK.jar . I put them into  /tool-data/shared/jars/gatk 
folder. I tested the installation following the instruction : 
http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
 


And I request a key from broadinstitute and followed the instruction on 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest

But the galaxy still gave me the error message as followed:

# ERROR 
--
# ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): 
# ERROR The invalid arguments or inputs must be corrected before the 
GATK can proceed
# ERROR Please do not post this error to the GATK forum
# ERROR
# ERROR See the documentation (rerun with -h) for this tool to view 
allowable command-line arguments.
# ERROR Visit our website and forum for extensive documentation and 
answers to 
# ERROR commonly asked questions http://www.broadinstitute.org/gatk
# ERROR
# ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option 
requires a GATK Key file. Please see 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 
for more information and instructions on how to obtain a key.
# ERROR 
--

I guess I may made mistakes in some point: 
1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. 
But I really don't know how to download and install it. I can't find the 
correct file. 
2. GATK2 works on Galaxy but I did something wrong on installing it. 

Could anyone help me about this? It will be greatly appreciated.

Thanks.

Anthonel
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Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread Fields, Christopher J
Older versions of GATK can be grabbed from Github:

https://github.com/broadgsa/gatk/tags

Not sure if they have an official 'older version' download site.

chris

On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote:

 Hi, 
 
 Could anyone give me some suggestions about that? 
 Thanks very much. 
 
 Anthonel 
 
 - Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM - 
 
 From:Yixiao Gong/cpdr/hjf 
 To:galaxy-dev@lists.bx.psu.edu 
 Date:12/12/2012 02:52 PM 
 Subject:Questions about Install GATK on local instance 
 
 
 Hi, all, 
 
 I'm installing GATK on galaxy local instance now and I have some questions 
 may need your help. 
 
 I downloaded the GATK2 from GATK website htt 
 http://www.broadinstitute.org/gatk/download  . the link is 
 http://www.broadinstitute.org/gatk/auth?package=GATK 
 
 I knew that on galaxy tool dependencies page 
 http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave the 
 link for GATK 1.4 version but I can't figure out how to download and install 
 it, and I noticed that GATK2 have all 1.x version features, so I installed 
 GATK2. 
 
 In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on 
 http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are 
 multiple folders and files and I got really confused what I need to download. 
 Even I choose ZIP to download a zip file, I counld not figure out whether 
 it is the program package and don't know how to install it. 
 
 Maybe this is the problem. But based on my understanding, GATK is just a set 
 of java package, and all we need to do is put it into /tool-data/shared/jars 
 folder, right? That is how I did it for GATK2. The GATK2 package include a 
 folder called resources and a file called GenomeAnalysisTK.jar . I put 
 them into  /tool-data/shared/jars/gatk folder. I tested the installation 
 following the instruction : 
 http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
  
 
 And I request a key from broadinstitute and followed the instruction on 
 http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
  
 
 But the galaxy still gave me the error message as followed: 
 
 # ERROR 
 --
 # ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): 
 # ERROR The invalid arguments or inputs must be corrected before the GATK 
 can proceed
 # ERROR Please do not post this error to the GATK forum
 # ERROR
 # ERROR See the documentation (rerun with -h) for this tool to view 
 allowable command-line arguments.
 # ERROR Visit our website and forum for extensive documentation and 
 answers to 
 # ERROR commonly asked questions http://www.broadinstitute.org/gatk
 # ERROR
 # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires 
 a GATK Key file. Please see 
 http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
  for more information and instructions on how to obtain a key.
 # ERROR 
 --
  
 
 I guess I may made mistakes in some point: 
 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. 
 But I really don't know how to download and install it. I can't find the 
 correct file. 
 2. GATK2 works on Galaxy but I did something wrong on installing it. 
 
 Could anyone help me about this? It will be greatly appreciated. 
 
 Thanks. 
 
 Anthonel ___
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Re: [galaxy-dev] Impersonate a User

2012-12-13 Thread greg
The problem is I disabled the logout button in universe.wsgi (I think)

(I believe I did that to make it compatible with LDAP?)

Thanks,

Greg

On Tue, Dec 11, 2012 at 5:00 PM, Edward Hills ehills...@gmail.com wrote:
 Hi Greg,

 Try clicking the logout button. That should logout of the user you are
 impersonating and back into you. Although, this does have a few quirks also
 and may log you right out. Don't forget that when you are impersonating
 someone the history may not be automatically loaded and you will have to do
 that manually.

 Cheers,
 Ed
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Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread ygong
Thanks very much, sir. 

Is there anything else I need to do specially for the setting up?

Best,

Anthonel



From:   Fields, Christopher J cjfie...@illinois.edu
To: yg...@cpdr.org yg...@cpdr.org
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:   12/13/2012 10:59 AM
Subject:Re: [galaxy-dev] Questions about Install GATK on local 
instance



Older versions of GATK can be grabbed from Github:

https://github.com/broadgsa/gatk/tags

Not sure if they have an official 'older version' download site.

chris

On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote:

 Hi, 
 
 Could anyone give me some suggestions about that? 
 Thanks very much. 
 
 Anthonel 
 
 - Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM - 
 
 From:Yixiao Gong/cpdr/hjf 
 To:galaxy-dev@lists.bx.psu.edu 
 Date:12/12/2012 02:52 PM 
 Subject:Questions about Install GATK on local instance 
 
 
 Hi, all, 
 
 I'm installing GATK on galaxy local instance now and I have some 
questions may need your help. 
 
 I downloaded the GATK2 from GATK website htt 
http://www.broadinstitute.org/gatk/download  . the link is 
http://www.broadinstitute.org/gatk/auth?package=GATK 
 
 I knew that on galaxy tool dependencies page 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave 
the link for GATK 1.4 version but I can't figure out how to download and 
install it, and I noticed that GATK2 have all 1.x version features, so I 
installed GATK2. 
 
 In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are 
multiple folders and files and I got really confused what I need to 
download. Even I choose ZIP to download a zip file, I counld not figure 
out whether it is the program package and don't know how to install it. 
 
 Maybe this is the problem. But based on my understanding, GATK is just a 
set of java package, and all we need to do is put it into 
/tool-data/shared/jars folder, right? That is how I did it for GATK2. The 
GATK2 package include a folder called resources and a file called 
GenomeAnalysisTK.jar . I put them into  /tool-data/shared/jars/gatk 
folder. I tested the installation following the instruction : 
http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
 

 
 And I request a key from broadinstitute and followed the instruction on 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 

 
 But the galaxy still gave me the error message as followed: 
 
 # ERROR 
--
 # ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): 
 # ERROR The invalid arguments or inputs must be corrected before the 
GATK can proceed
 # ERROR Please do not post this error to the GATK forum
 # ERROR
 # ERROR See the documentation (rerun with -h) for this tool to view 
allowable command-line arguments.
 # ERROR Visit our website and forum for extensive documentation and 
answers to 
 # ERROR commonly asked questions http://www.broadinstitute.org/gatk
 # ERROR
 # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option 
requires a GATK Key file. Please see 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 
for more information and instructions on how to obtain a key.
 # ERROR 
--
 

 
 I guess I may made mistakes in some point: 
 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use 
it. But I really don't know how to download and install it. I can't find 
the correct file. 
 2. GATK2 works on Galaxy but I did something wrong on installing it. 
 
 Could anyone help me about this? It will be greatly appreciated. 
 
 Thanks. 
 
 Anthonel ___
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Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread ygong
Yes, sir. I downloaded the 1.4 version from Chris's link 
https://github.com/broadgsa/gatk/tags, it looks the same as the one that I 
saw on the https://github.com/broadgsa/gatk. I couldn't figure out how to 
intall it because it contains two folders and multiple files except any 
executable. How do I install it? What configuration I need to do to make 
it work on Galaxy? 

Thanks very much.

Anthonel



From:   yg...@cpdr.org
To: Fields, Christopher J cjfie...@illinois.edu
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:   12/13/2012 11:02 AM
Subject:Re: [galaxy-dev] Questions about Install GATK on local 
instance
Sent by:galaxy-dev-boun...@lists.bx.psu.edu



Thanks very much, sir. 

Is there anything else I need to do specially for the setting up? 

Best, 

Anthonel 



From:Fields, Christopher J cjfie...@illinois.edu 
To:yg...@cpdr.org yg...@cpdr.org 
Cc:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 
Date:12/13/2012 10:59 AM 
Subject:Re: [galaxy-dev] Questions about Install GATK on local 
instance 



Older versions of GATK can be grabbed from Github:

https://github.com/broadgsa/gatk/tags

Not sure if they have an official 'older version' download site.

chris

On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote:

 Hi, 
 
 Could anyone give me some suggestions about that? 
 Thanks very much. 
 
 Anthonel 
 
 - Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM - 
 
 From:Yixiao Gong/cpdr/hjf 
 To:galaxy-dev@lists.bx.psu.edu 
 Date:12/12/2012 02:52 PM 
 Subject:Questions about Install GATK on local instance 
 
 
 Hi, all, 
 
 I'm installing GATK on galaxy local instance now and I have some 
questions may need your help. 
 
 I downloaded the GATK2 from GATK website htt 
http://www.broadinstitute.org/gatk/download  . the link is 
http://www.broadinstitute.org/gatk/auth?package=GATK 
 
 I knew that on galaxy tool dependencies page 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave 
the link for GATK 1.4 version but I can't figure out how to download and 
install it, and I noticed that GATK2 have all 1.x version features, so I 
installed GATK2. 
 
 In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on 
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are 
multiple folders and files and I got really confused what I need to 
download. Even I choose ZIP to download a zip file, I counld not figure 
out whether it is the program package and don't know how to install it. 
 
 Maybe this is the problem. But based on my understanding, GATK is just a 
set of java package, and all we need to do is put it into 
/tool-data/shared/jars folder, right? That is how I did it for GATK2. The 
GATK2 package include a folder called resources and a file called 
GenomeAnalysisTK.jar . I put them into  /tool-data/shared/jars/gatk 
folder. I tested the installation following the instruction : 
http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-installation
 

 
 And I request a key from broadinstitute and followed the instruction on 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 

 
 But the galaxy still gave me the error message as followed: 
 
 # ERROR 
--
 # ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): 
 # ERROR The invalid arguments or inputs must be corrected before the 
GATK can proceed
 # ERROR Please do not post this error to the GATK forum
 # ERROR
 # ERROR See the documentation (rerun with -h) for this tool to view 
allowable command-line arguments.
 # ERROR Visit our website and forum for extensive documentation and 
answers to 
 # ERROR commonly asked questions http://www.broadinstitute.org/gatk
 # ERROR
 # ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option 
requires a GATK Key file. Please see 
http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me#latest
 
for more information and instructions on how to obtain a key.
 # ERROR 
--
 

 
 I guess I may made mistakes in some point: 
 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use 
it. But I really don't know how to download and install it. I can't find 
the correct file. 
 2. GATK2 works on Galaxy but I did something wrong on installing it. 
 
 Could anyone help me about this? It will be greatly appreciated. 
 
 Thanks. 
 
 Anthonel ___
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Re: [galaxy-dev] Impersonate a User

2012-12-13 Thread Fields, Christopher J
The user impersonation feature doesn't work with external authentication.  
There is a bug report on this:

https://trello.com/c/zwqNwflD

chris

On Dec 13, 2012, at 10:01 AM, greg margeem...@gmail.com wrote:

 The problem is I disabled the logout button in universe.wsgi (I think)
 
 (I believe I did that to make it compatible with LDAP?)
 
 Thanks,
 
 Greg
 
 On Tue, Dec 11, 2012 at 5:00 PM, Edward Hills ehills...@gmail.com wrote:
 Hi Greg,
 
 Try clicking the logout button. That should logout of the user you are
 impersonating and back into you. Although, this does have a few quirks also
 and may log you right out. Don't forget that when you are impersonating
 someone the history may not be automatically loaded and you will have to do
 that manually.
 
 Cheers,
 Ed
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Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-13 Thread Sarah Maman

Hi Daniel,

In fact, my version needs to be updated :

changeset:   6799:40f1816d6857
tag: tip
user:Greg Von Kuster g...@bx.psu.edu
date:Wed Mar 07 13:35:34 2012 -0500
summary: Fix for populating the tool panel and generating the  
integrated_tool_panel.xml file.


I try and let you know.
Sarah

Daniel Blankenberg d...@bx.psu.edu a écrit :


Hi Sarah,

This looks to be due to a non-unicode character in the dataset's  
info field. Are you using a Galaxy revision = 7563:fca4e12478d6?



Thanks for using Galaxy,

Dan


On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote:


Hello,

One of my users gets the following message when he wishes to edit  
the attribute of a dataset which is generated by using a tool (same  
problem as it is a tool provided by Galaxy or a tool coded by us).


Do you have any idea?

Thanks in advance,
Sarah Maman

URL:  
http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in  
__call__

app_iter = self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in  
__call__

environ, self.app)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in  
intercept_output

app_iter = application(environ, replacement_start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in  
__call__

return self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in  
__call__

return self.app( environ, start_response )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in  
__call__

return self.application(environ, start_response)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in  
__call__

body = method( trans, **kwargs )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in  
edit

refresh_frames=refresh_frames )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in  
fill_template

return self.fill_template_mako( filename, **kwargs )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in  
fill_template_mako

return template.render( **data )
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in  
render

return runtime._render(self, self.callable_, args, data)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in  
_render

**_kwargs_for_callable(callable_, data))
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in  
_render_context

_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in  
_exec_template

callable_(context, *args, **kwargs)
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in  
render_body

__M_writer(unicode(next.body()))
File  
'/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in  
render_body

__M_writer(filters.html_escape(unicode(data.info )))
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in  
position 31: ordinal not in range(128)

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--
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel:   +33(0)5.61.28.57.08
Fax:   +33(0)5.61.28.57.53

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[galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg
I'm seeing the error below when I try to run Tophat for Illumina.

Has anyone seen this before?  Could I have installed bowtie
incorrectly or am I simply running with the wrong data/parameters?

Thanks,

Greg

(I'm also really confused why the error is mentioned /tmp/* paths.  I
never assigned anything to /tmp in the universe_wsgi.ini.  Where is it
getting that from?)


Error in tophat:

[2012-12-13 13:55:01] Beginning TopHat run (v2.0.6)
---
[2012-12-13 13:55:01] Checking for Bowtie
 Bowtie version: 2.0.2.0
[2012-12-13 13:55:01] Checking for Samtools
  Samtools version: 0.1.18.0
[2012-12-13 13:55:01] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
(/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)
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Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Lance Parsons
Since I've had issues with workflow and the toolshed in the past, I have 
changed my workflow so that my only interaction with the toolshed is 
either via uploading a tarball via the web interface or installing a 
tool into my local Galaxy via the web interface (or occasionally just 
downloading tarballs).


In this specific case, I uploaded a tar.gz file of the entire tool 
wrapper directory.  I did NOT increment the tool version.  In the past, 
incrementing the tool version has generally worked fine.  However, when 
I leave the tool version the same, but change something (such as the 
help text for the tool), and then upload a tarball to the toolshed, I am 
unable to pull updates into my local galaxy instance.  I get an error 
similar to what I have described.


I hope this is enough information, but let me know if I can provide more 
detail, etc.  I would very much like to get to the root of this issue, 
since it has plagued my attempts to use the toolshed smoothly when 
(seemingly inevitable) minor changes need to be made.  In the past I 
have just had to wait until I update the tool version, as no changes can 
be made to the installed revision in my production Galaxy instance.


Greg Von Kuster wrote:

Hi Lance,

What process did you use for updating the tool shed repository and how many 
separate repositories did you use?  You should not be updating a local 
repository, pushing the changes to the tool shed repository, and then 
attempting to pull the changes back to the same repository.  Your repository 
environment should be something like this:

DEV REPO ( all development updates are performed here, so this is where the 
tool version is incremented )
 |
V
pushed changeset
|
V
EXISTING TOOL SHED REPO
|
   V
pulled changeset to some previously cloned repo
|
   V
PREVIOUSLY CLONED (possibly production) REPO

In other words, nothing should ever get pushed and pulled from the tool shed 
repo into the same repo.  If this is the process you used, it would undoubtedly 
result in the behavior you saw.  If you used separate repos as I describe 
above, we'll need more details as to the process you used in order to determine 
the cause of the problem.

Greg Von Kuster


On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:


I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3.  
This version has some functional changes and thus the tool version was 
incremented.  I installed this new version of the tool in my local Galaxy 
instance.

However, I realized later that I missed updating one part of the help text. Today I fixed 
that text (but left the tool version the same), tarred up the file, and uploaded it to 
the toolshed.  I then attempted to Get Updates from my local Galaxy instances 
for that tool got the following error:

URL: 
http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/name=htseq_countowner=lparsonschangeset_revision=5d969cb56112latest_changeset_revision=f320093f1e8elatest_ctx_rev=11
File 
'/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
 line 364 in respond
app_iter = self.application(environ, detect_start_response)
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', 
line 98 in __call__
environ, self.app)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 
line 539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
line 80 in __call__
return self.application(environ, start_response)
File 
'/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
 line 91 in __call__
return self.app( environ, start_response )
File 
'/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', 
line 632 in __call__
return self.application(environ, start_response)
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 
in __call__
body = method( trans, **kwargs )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 
206 in decorator
return func( self, trans, *args, **kwargs )
File 
'/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
 line 1677 in update_to_changeset_revision
update_repository( repo, latest_ctx_rev )
File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', line 
1428 in update_repository
rev=ctx_rev )
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py',
 line 5661 in update
rev = scmutil.revsingle(repo, rev, rev).rev()
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
 line 515 in revsingle
l = revrange(repo, [revspec])
File 
'/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py',
 

Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg
I'm confused.  So I installed tophat-2.0.6.Linux_x86_64 which seems to
contain tophat and tophat2.  Can't galaxy use that tophat?

Am I supposed to also install tophat 1?  Does galaxy somehow failover
to use tophat2 otherwise?  What am I missing?

Thanks,

Greg

On Thu, Dec 13, 2012 at 2:32 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:

 On Dec 13, 2012, at 2:13 PM, greg wrote:

 I'm seeing the error below when I try to run Tophat for Illumina.

 Has anyone seen this before?  Could I have installed bowtie
 incorrectly or am I simply running with the wrong data/parameters?

 You are using Tophat2, not Tophat (note the version at the beginning of the 
 log). You can either

 (a) install and use Tophat 1.X

 or

 (b) use the Tophat2 wrapper in conjunction with Bowtie2.

 For (a), you'll want to modify the bowtie_indices.loc; for (b), modify 
 bowtie2_indices.loc

 J.


 Thanks,

 Greg

 (I'm also really confused why the error is mentioned /tmp/* paths.  I
 never assigned anything to /tmp in the universe_wsgi.ini.  Where is it
 getting that from?)


 Error in tophat:

 [2012-12-13 13:55:01] Beginning TopHat run (v2.0.6)
 ---
 [2012-12-13 13:55:01] Checking for Bowtie
 Bowtie version: 2.0.2.0
 [2012-12-13 13:55:01] Checking for Samtools
  Samtools version: 0.1.18.0
 [2012-12-13 13:55:01] Checking for Bowtie index files
 Error: Could not find Bowtie 2 index files
 (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)
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Re: [galaxy-dev] Downloading datasets without username/password when login is required

2012-12-13 Thread Sytchev, Ilya
So, it turns out that it's currently impossible to download datasets
programmatically without using username/password (when require_login is
set to True) because Galaxy API does not have functionality to download
datasets.  Are there any plans to implement this feature?

Thanks,
Ilya


On 12/11/12 2:41 PM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote:

Hi,

Is it possible to download a dataset when require_login=True in
universe_wsgi.ini using the API key?

Thanks,
Ilya



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Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread Jeremy Goecks

 I'm confused.  So I installed tophat-2.0.6.Linux_x86_64 which seems to
 contain tophat and tophat2.  

tophat2 redirects to tophat, which is tophat version 2.X.X

 Can't galaxy use that tophat?

You can, but you need to use the Tophat2 wrapper, not the Tophat for Illumina 
wrapper. And, when you use the Tophat2 wrapper, you'll need to have Bowtie2 
installed and the bowtie2_indices.loc set up appropriately.

J.
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Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Greg Von Kuster
Hi Lance,

I tried several scenarios today in an attempt to reproduce this but I was not 
able to.  Have you tried uninstalling the repository (check the checkbox to 
completely uninstall it) and then reinstall it?  I'm trying to reproduce this 
on a mac running mercurial version 2.2.3 and Python 2.5.  What's your 
environment?

Greg Von Kuster


On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote:

 Since I've had issues with workflow and the toolshed in the past, I have 
 changed my workflow so that my only interaction with the toolshed is either 
 via uploading a tarball via the web interface or installing a tool into my 
 local Galaxy via the web interface (or occasionally just downloading 
 tarballs).
 
 In this specific case, I uploaded a tar.gz file of the entire tool wrapper 
 directory.  I did NOT increment the tool version.  In the past, incrementing 
 the tool version has generally worked fine.  However, when I leave the tool 
 version the same, but change something (such as the help text for the tool), 
 and then upload a tarball to the toolshed, I am unable to pull updates into 
 my local galaxy instance.  I get an error similar to what I have described.
 
 I hope this is enough information, but let me know if I can provide more 
 detail, etc.  I would very much like to get to the root of this issue, since 
 it has plagued my attempts to use the toolshed smoothly when (seemingly 
 inevitable) minor changes need to be made.  In the past I have just had to 
 wait until I update the tool version, as no changes can be made to the 
 installed revision in my production Galaxy instance.
 
 Greg Von Kuster wrote:
 
 Hi Lance,
 
 What process did you use for updating the tool shed repository and how many 
 separate repositories did you use?  You should not be updating a local 
 repository, pushing the changes to the tool shed repository, and then 
 attempting to pull the changes back to the same repository.  Your repository 
 environment should be something like this:
 
 DEV REPO ( all development updates are performed here, so this is where the 
 tool version is incremented )
 |
V
 pushed changeset
|
V
 EXISTING TOOL SHED REPO
|
   V
 pulled changeset to some previously cloned repo
|
   V
 PREVIOUSLY CLONED (possibly production) REPO
 
 In other words, nothing should ever get pushed and pulled from the tool shed 
 repo into the same repo.  If this is the process you used, it would 
 undoubtedly result in the behavior you saw.  If you used separate repos as I 
 describe above, we'll need more details as to the process you used in order 
 to determine the cause of the problem.
 
 Greg Von Kuster
 
 
 On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:
 
 I recently updated the htseq-count tool in the Galaxy toolshed to version 
 0.3.  This version has some functional changes and thus the tool version 
 was incremented.  I installed this new version of the tool in my local 
 Galaxy instance.
 
 However, I realized later that I missed updating one part of the help text. 
 Today I fixed that text (but left the tool version the same), tarred up the 
 file, and uploaded it to the toolshed.  I then attempted to Get Updates 
 from my local Galaxy instances for that tool got the following error:
 
 URL: 
 http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision?tool_shed_url=http://toolshed.g2.bx.psu.edu/name=htseq_countowner=lparsonschangeset_revision=5d969cb56112latest_changeset_revision=f320093f1e8elatest_ctx_rev=11
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
  line 364 in respond
 app_iter = self.application(environ, detect_start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py',
  line 98 in __call__
 environ, self.app)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', 
 line 539 in intercept_output
 app_iter = application(environ, replacement_start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', 
 line 80 in __call__
 return self.application(environ, start_response)
 File 
 '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py',
  line 91 in __call__
 return self.app( environ, start_response )
 File 
 '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
  line 632 in __call__
 return self.application(environ, start_response)
 File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 
 160 in __call__
 body = method( trans, **kwargs )
 File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', 
 line 206 in decorator
 return func( self, trans, *args, **kwargs )
 File 
 '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
  line 1677 in update_to_changeset_revision
 update_repository( repo, latest_ctx_rev )
 File 

[galaxy-dev] tools imported from toolshed stay in waiting to run status

2012-12-13 Thread Philipe Moncuquet
Hi dev,

We are running a local instance of Galaxy, last update was the November
release (7148:17d57db9a7c0 I think). We are facing problem when trying to
run tools that were imported via the toolshed. The never start and the
status stays on waiting to run. Other tools work fine, and this generic
to all tools from toolshed. Any suggestions on where should I look to fix
this ?

Philippe
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