Re: [galaxy-dev] public datasets/histories with external auth

[Shantanu Pavgi]

On Jun 28, 2011, at 2:15 PM, Nate Coraor wrote:

Shantanu Pavgi wrote:

I did a test by excluding following URLs from Apache-Shibboleth external 
authentication and it seems to be working:
-  /datasets/
-  /u//h/
- /static/  (css and javascript)

Do I need to exclude any other URLs so that published histories and datasets 
can be accessed from remote sites without authentication? Also, will it offer 
read-only access to the galaxy interface? Does it expose any job submission, 
file-uploads or any other modification/execution operations using web interface?

Hi Shantanu,

These should be sufficient and would not give access to anything job or
tool related.  However, since /datasets/ is exposed, this means that any
dataset with no roles associated with the access permission (i.e. a
"public" dataset) would be readable by anyone.  Dataset IDs are encoded
so as not to be easily guessable, but relying on this is essentially
"security by obscurity."


Thanks for the reply Nate. We are able to view datasets over to UCSC site if we 
directly append /dataset URL as a query parameter to the main UCSC URL. But we 
discovered one more use case where datasets contained in a particular history 
have a different URL format for UCSC link.

For example, you should be able to access following URL without authentication:
https://galaxy.uabgrid.uab.edu/history/list_shared?sort=-update_time&operation=View&id=24d84bcf64116fe7

Now if you click on dataset-1 and then click on 'display at UCSC main' then the 
resulting URL is as follows:

https://galaxy.uabgrid.uab.edu/datasets/3423/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm9%26position%3Dchr1%3A20048750-20608024%26hgt.customText%3D%25s&display_url=http%3A%2F%2Fgalaxy.uabgrid.uab.edu%2Froot%2Fdisplay_as%3Fid%3D3423%26display_app%3Ducsc%26authz_method%3Ddisplay_at

This link fails without authentication as we have exposed only /datasets URL 
pattern. I can manually insert /dataset URL for UCSC 'display_url', however 
it's not intuitive for end users. I am bit concerned about opening up 
"/root/display_as" URL pattern without knowing it's implications. I guess it 
doesn't expose any jobs or tools related access, but not sure about it. Any 
comments or suggestions?



Also, can we prevent particular galaxy-user from carrying out certain actions, 
e.g. running jobs, file uploads etc.? Since galaxy will create 'anonymous' user 
account based on the REMOTE_USER variable set for unauthenticated requests, I 
am wondering if such locked-down mode will be possible for a particular 
galaxy-user.

This cannot be done from within Galaxy, but it shouldn't be necessary
since these actions are not exposed to the anonymous user.

I think the user is not anonymous here as we have already written REMOTE_USER 
to 'anonymous' now. The galaxy receives this user as user-login/email as 
'anonymous@mail.domain'.

Now we are opening up certain URL patterns to be accessed as 
'anonymous@mail.domain' user. These URL patterns 
include following formats as mentioned - /datasets, /history, 
/u//h, and /static. In addition we may need to expose 
"/root/display_as" URL pattern as well. Rest of the site remains protected 
using real authentication.
So as long as above URL patterns don't expose any job submission, file uploads 
or other galaxy tools operations then we should be OK with it. Thoughts?

--
Thanks,
Shantanu.

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Re: [galaxy-dev] public datasets/histories with external auth

[Shantanu Pavgi]

On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:

Leandro Hermida wrote:
Hi Shantanu,

In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path?  I'm just
looking at the Apache docs and the RequestHeader directive has a context of
the entire VirtualHost and cannot be put into a Location container so I'm
not sure how to do it.

Hi Leandro,

See the optional 'env=' argument and docs on the same for ways to make
RequestHeader conditional:

   http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader

So, depending on the path accessed, you should be able to have
mod_rewrite set an environment variable specifying which REMOTE_USER
(real username or fake anonymouse user) should be set.

You could also just set it as the anonymous user to start with and then
use 'RequestHeader set' to overwrite it with the real username in the
case that a real username is available.

This is all just from glancing at the docs, though, I have not tried any
of it out, and this sort of Apache trickery is always difficult to get
right.

--nate



Leandro,

The RequestHeader has a context of 'directory' as well, which includes 
, , , and  containers [1]. So you should be 
able to use it in Location directive.

Following is a configuration snippet related to what Nate described in his 
earlier response. We are setting REMOTE_USER variable to anonymous when it's 
not set/empty.

AuthType shibboleth
ShibRequireSession off
Require shibboleth
RewriteCond %{LA-U:REMOTE_USER} =""
RequestHeader set REMOTE_USER "anonymous"


Hope this helps.


1. http://httpd.apache.org/docs/current/mod/directive-dict.html#Context

--
Shantanu.

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Re: [galaxy-dev] Question about installing NCBI BLAST+ onto Galaxy

[Peter Cock]

On Tue, Jun 28, 2011 at 9:52 PM, George Michopoulos
 wrote:
> Hey everyone,
> Hope all is well! I was wondering if someone could help me with
> another error I ran into. I recently downloaded the NCBI BLAST+ toolkit and
> it automatically installed itself into Galaxy. I'm just wondering if anyone
> knows where I am supposed to put the directory with the database files it
> needs to run correctly, or if it makes a difference.

It shouldn't matter as long a you use an appropriate path in the
blastdb.loc and blastdb_p.loc files. We use /data/blastdb/ for ours.

> I have configured the
> blastdb.loc file as shown below, and the database now appears in the
> drop-down menu for the NCBI tools, but when I try executing any of the
> BLASTs Galaxy returns the following error, regardless of the path
> permutation I try:

At least Galaxy is finding the loc file :)

> When I tried putting the databases within the galaxy installation (within
> galaxy_test) and I used the whole path:
> BLAST Database error: No alias or index file found for nucleotide
> database [/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna] in
> search path
> [/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/job_working_directory/28::]
> Return error code 2 from command: tblastx -query
> /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/files/000/dataset_27.dat -db
> "/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna"
> -evalue 0.001 -out
> /Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/database/files/000/dataset_32.dat -outfmt
> 6 -num_threads 8

Does BLAST+ work at the command line?

Does BLAST+ work within Galaxy for FASTA vs FASTA (rather than
FASTA vs database)?

Also what does this give:

ls 
/Users/burtonigenomics/Rosa_Files/bin/fastx_bin/galaxy_test/tool-data/blastdb/refseq_rna.*

My guess is you have tried a valid path, but that the Galaxy user does
not have read permission so BLAST+ can't open the database.

Peter

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Re: [galaxy-dev] changing file storage location

[Enis Afgan]

In the string, I assumed 'galaxy' to be the username for accessing the
database.
The string is standard SQLalchemy connection string:
http://www.sqlalchemy.org/docs/core/engines.html#engine-creation-api


On Wed, Jun 29, 2011 at 5:11 PM, Sanka, Ravi  wrote:

> Yes, I saw in the documentation that PostrgeSQL is preferred. For the time
> being, however, I only have access to MYSQL.
>
> ** **
>
> I noticed in your example URL, there is no spot for username, only
> password, host, and socket. Does Galaxy not require a username for
> connecting to a MYSQL database?
>
> ** **
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
> ** **
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 5:06 PM
>
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
> ** **
>
> Almost, mysql requires two forward slashes, like so:
>
> database_connection = mysql://galaxy:password_here@
> /galaxy?unix_socket=/var/run/mysqld/mysqld.sock
>
> ** **
>
> NTW, unless you are not absolutely set on MySQL, the Galaxy team prefers
> PostrgeSQL as the backend database. 
>
> ** **
>
> Enis
>
> ** **
>
> On Wed, Jun 29, 2011 at 4:03 PM, Sanka, Ravi  wrote:
>
> Hello Enis,
>
>  
>
> Thank you. Galaxy is now directing the files to the new storage location.*
> ***
>
>  
>
> On a related note, I am also planning to switch Galaxy from the default
> SQLite to an existing MYSQL database. The documentation says to do this, the
> database_connection field in the config file must be given the proper URL.
> This is the example it gave:
>
>  
>
> database_connection =
> postgres:///
>
>  
>
> Would the same value work if postgres was switched out with mysql?
>
>  
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
>  
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 12:02 PM
>
>
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
>  
>
> In order for Galaxy to acknowledge the changes, you'll have to restart
> Galaxy. I'll double check in the wiki to make sure this is stated somewhere
> but simply stopping the Galaxy process and starting it back up should reload
> the config file. 
>
>  
>
> If your Galaxy is running the background run:
>
> sh run.sh --stop-daemon
>
> sh run.sh --daemon
>
>  
>
> If the process is not running in the background, simply stop it (i.e., ctrl
> + C)
>
>  
>
> Enis
>
> On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi  wrote:
>
> Hi Enis,
>
>  
>
> No I didn’t restart Galaxy after the changes were saved. Is that the
> process explained in the README.txt (setup.sh & run.sh)? That process was
> for the first time, so I didn’t repeat it after saving the changes.
>
>  
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
>  
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 11:32 AM
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
>  
>
> Hi Ravi,
>
> Just a quick check - did you restart Galaxy after saving the changes? What
> you did should direct any new files to the specified location.
>
>  
>
> Enis
>
> On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi  wrote:
>
> Greetings,
>
>  
>
> My name is Ravi Sanka. I have a question regarding Galaxy.
>
>  
>
> Recently, I had a local installation set up and am now trying to change the
> location where the install stores imported and created files.
>
>  
>
> I opened the config file universe_wsgi.ini and did the following:
>
>  
>
> -  Removed the ‘#’ mark from ‘#file_path = database/files’
>
> -  Changed value of file_path to the absolute path of an
> accessible, readable/writable location
>
> -  Saved changes
>
>  
>
> Despite this, the install still stores files in database/files. Is there a
> step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be
> run again?
>
>  
>
> I also intend to change the database from the SQLite default to an existing
> database, so I assume the steps to change the file_path also apply to
> database_connection.
>
>  
>
> Thank you for your time.
>
>  
>
> -

Re: [galaxy-dev] changing file storage location

[Enis Afgan]

Almost, mysql requires two forward slashes, like so:
database_connection = mysql://galaxy:password_here@
/galaxy?unix_socket=/var/run/mysqld/mysqld.sock

NTW, unless you are not absolutely set on MySQL, the Galaxy team prefers
PostrgeSQL as the backend database.

Enis

On Wed, Jun 29, 2011 at 4:03 PM, Sanka, Ravi  wrote:

> Hello Enis,
>
> ** **
>
> Thank you. Galaxy is now directing the files to the new storage location.*
> ***
>
> ** **
>
> On a related note, I am also planning to switch Galaxy from the default
> SQLite to an existing MYSQL database. The documentation says to do this, the
> database_connection field in the config file must be given the proper URL.
> This is the example it gave:
>
> ** **
>
> database_connection =
> postgres:///
>
> ** **
>
> Would the same value work if postgres was switched out with mysql?
>
> ** **
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
> ** **
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 12:02 PM
>
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
> ** **
>
> In order for Galaxy to acknowledge the changes, you'll have to restart
> Galaxy. I'll double check in the wiki to make sure this is stated somewhere
> but simply stopping the Galaxy process and starting it back up should reload
> the config file. 
>
> ** **
>
> If your Galaxy is running the background run:
>
> sh run.sh --stop-daemon
>
> sh run.sh --daemon
>
> ** **
>
> If the process is not running in the background, simply stop it (i.e., ctrl
> + C)
>
> ** **
>
> Enis
>
> On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi  wrote:
>
> Hi Enis,
>
>  
>
> No I didn’t restart Galaxy after the changes were saved. Is that the
> process explained in the README.txt (setup.sh & run.sh)? That process was
> for the first time, so I didn’t repeat it after saving the changes.
>
>  
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
>  
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 11:32 AM
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
>  
>
> Hi Ravi,
>
> Just a quick check - did you restart Galaxy after saving the changes? What
> you did should direct any new files to the specified location.
>
>  
>
> Enis
>
> On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi  wrote:
>
> Greetings,
>
>  
>
> My name is Ravi Sanka. I have a question regarding Galaxy.
>
>  
>
> Recently, I had a local installation set up and am now trying to change the
> location where the install stores imported and created files.
>
>  
>
> I opened the config file universe_wsgi.ini and did the following:
>
>  
>
> -  Removed the ‘#’ mark from ‘#file_path = database/files’
>
> -  Changed value of file_path to the absolute path of an
> accessible, readable/writable location
>
> -  Saved changes
>
>  
>
> Despite this, the install still stores files in database/files. Is there a
> step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be
> run again?
>
>  
>
> I also intend to change the database from the SQLite default to an existing
> database, so I assume the steps to change the file_path also apply to
> database_connection.
>
>  
>
> Thank you for your time.
>
>  
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
>  
>
>
> ___
> 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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Re: [galaxy-dev] changing file storage location

[Sanka, Ravi]

Hello Enis,

Thank you. Galaxy is now directing the files to the new storage location.

On a related note, I am also planning to switch Galaxy from the default SQLite 
to an existing MYSQL database. The documentation says to do this, the 
database_connection field in the config file must be given the proper URL. This 
is the example it gave:

database_connection = postgres:///

Would the same value work if postgres was switched out with mysql?

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---

From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Wednesday, June 29, 2011 12:02 PM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] changing file storage location

In order for Galaxy to acknowledge the changes, you'll have to restart Galaxy. 
I'll double check in the wiki to make sure this is stated somewhere but simply 
stopping the Galaxy process and starting it back up should reload the config 
file.

If your Galaxy is running the background run:
sh run.sh --stop-daemon
sh run.sh --daemon

If the process is not running in the background, simply stop it (i.e., ctrl + C)

Enis
On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi 
mailto:rsa...@jcvi.org>> wrote:
Hi Enis,

No I didn't restart Galaxy after the changes were saved. Is that the process 
explained in the README.txt (setup.sh & run.sh)? That process was for the first 
time, so I didn't repeat it after saving the changes.

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---

From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Wednesday, June 29, 2011 11:32 AM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] changing file storage location

Hi Ravi,
Just a quick check - did you restart Galaxy after saving the changes? What you 
did should direct any new files to the specified location.

Enis
On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi 
mailto:rsa...@jcvi.org>> wrote:
Greetings,

My name is Ravi Sanka. I have a question regarding Galaxy.

Recently, I had a local installation set up and am now trying to change the 
location where the install stores imported and created files.

I opened the config file universe_wsgi.ini and did the following:


-  Removed the '#' mark from '#file_path = database/files'

-  Changed value of file_path to the absolute path of an accessible, 
readable/writable location

-  Saved changes

Despite this, the install still stores files in database/files. Is there a step 
I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again?

I also intend to change the database from the SQLite default to an existing 
database, so I assume the steps to change the file_path also apply to 
database_connection.

Thank you for your time.

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---


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Re: [galaxy-dev] bwa failure preparing job

[Kelly Vincent]

Branden,

Sorry for the delay in response. Have you gotten things working yet?  
If not, what changeset are you on now? The data tables issue is what's  
going on here. But it's odd that you're still seeing "from_file" in  
BWA and Bowtie, because they (plus all NGS tools except the samtools  
ones) have been using data tables for some time. Let us know if you  
are still having problems with this.


Thanks,
Kelly


On Tue Apr 26, at 5:11 PM, Branden Timm wrote:


Vipin, thanks for the tip.  I was not aware of data tables at all.

I checked bwa_wrapper.xml and it is still using the from_file  
attribute for the reference genome parameter, not from_data_table.   
It would appear then that BWA is not using data tables?   
Additionally, I have now noticed that our bowtie runs are failing as  
well with the error:


AssertionError: Requested 'path' column missing from column def

I looked at bowtie_wrapper.xml, and it too seems to still be using  
from_file instead of from_data_table for the reference genome drop- 
down.  There is a line there using data tables, but it is commented  
out:




I'm really confused as to what is going on here, but it seems like  
when I updated recently (first time since January probably) it broke  
all of my location files and I'm not sure how to fix them.  I'm also  
confused because it seems that even using data tables, the format of  
my .loc files shouldn't need to change because they both use four  
columns separated by tabs.


As always, any help is greatly appreciated.

--
Branden Timm
bt...@glbrc.wisc.edu


On 4/26/2011 12:29 PM, Vipin TS wrote:


Hi Branden,

I find a wiki documentation here,

https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables

Hope this will help you to experiment a bit around.

regards, Vipin

Does anybody have any idea why I would be getting this error before  
the tool runs?


--
Branden Timm
Great Lakes Bioenergy Research Center
bt...@wisc.edu


On 4/19/2011 10:45 AM, Branden Timm wrote:

Hi All,
  I'm having issues running BWA for Illumina with the latest  
version of Galaxy (5433:c1aeb2f33b4a).


It seems that the error is a python list error while preparing the  
job:


 Traceback (most recent call last):
  File "/home/galaxy/galaxy-central/lib/galaxy/jobs/runners/ 
local.py", line 58, in run_job

job_wrapper.prepare()
  File "/home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py",  
line 371, in prepare

self.command_line = self.tool.build_command_line( param_dict )
  File "/home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py",  
line 1575, in build_command_line

command_line = fill_template( self.command, context=param_dict )
  File "/home/galaxy/galaxy-central/lib/galaxy/util/template.py",  
line 9, in fill_template
return str( Template( source=template_text,  
searchList=[context] ) )
  File "/home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux- 
x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__

return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 106, in respond
IndexError: list index out of range
I checked the bwa_index.loc file for errors, it seems that the  
line for the reference genome I'm trying to map against is correct  
(all whitespace is tab characters):
synpcc7002  synpcc7002  Synechococcus   /home/galaxy/ 
galaxy-central/bwa_

indices/SYNPCC7002

I'm not sure what the next troubleshooting step is, any ideas?

--
Branden Timm
bt...@glbrc.wisc.edu

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Re: [galaxy-dev] assembly statistics dependencies

[Anton Nekrutenko]

Yann:

These tools are for testing only, and not yet supported/distributed.

Thanks,

anton


Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Jun 25, 2011, at 11:11 PM, Yann Surget-Groba wrote:

> Dear all,
> I'm trying to use the tool assembly statistics in the 'PacBio/Illumina 
> Assembly' section but I have the following error message:
> Traceback (most recent call last):
> File "/home/galaxy/galaxy_dist/tools/ilmn_pacbio/assembly_stats.py", line 7, 
> in 
> from pbpy.io.FastaIO import FastaEntry, SimpleFastaReader
> ImportError: No module named pbpy.io.FastaIO
>  
> Can someone tell me where to find the module pbpy, I couldn't find this 
> information in the Galaxy wiki.
> Thanks in advance,
> Yann
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Re: [galaxy-dev] public datasets/histories with external auth

[Nate Coraor]

Leandro Hermida wrote:
> Hi Shantanu,
> 
> In your Apache configuration exactly how did you set up an anonymous
> REMOTE_USER just for specific locations like the /datasets/ path?  I'm just
> looking at the Apache docs and the RequestHeader directive has a context of
> the entire VirtualHost and cannot be put into a Location container so I'm
> not sure how to do it.

Hi Leandro,

See the optional 'env=' argument and docs on the same for ways to make
RequestHeader conditional:

http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader

So, depending on the path accessed, you should be able to have
mod_rewrite set an environment variable specifying which REMOTE_USER
(real username or fake anonymouse user) should be set.

You could also just set it as the anonymous user to start with and then
use 'RequestHeader set' to overwrite it with the real username in the
case that a real username is available.

This is all just from glancing at the docs, though, I have not tried any
of it out, and this sort of Apache trickery is always difficult to get
right.

--nate

> 
> thanks,
> Leandro
> 
> On Wed, Jun 22, 2011 at 9:40 PM, Shantanu Pavgi  wrote:
> 
> >
> > On Jun 20, 2011, at 4:10 PM, Shantanu Pavgi wrote:
> >
> > >
> > > On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote:
> > >
> > >> Shantanu Pavgi wrote:
> > >>> Hi,
> > >>>
> > >>> We have a galaxy server setup using external shibboleth authentication.
> > While we would like to have site behind authentication realm, there are
> > instances when our galaxy datasets/histories need to be accessible publicly
> > from other websites. We tried adding an exception to auth rule for /datasets
> >  path using Location directive in apache web server configuration, however
> > galaxy server returned an error as:
> > >>>
> > >>> {{{
> > >>> Access to Galaxy is denied
> > >>> Galaxy is configured to authenticate users via an external method (such
> > as HTTP authentication in Apache), but a username was not provided by the
> > upstream (proxy) server. This is generally due to a misconfiguration in the
> > upstream server.
> > >>> }}}
> > >>>
> > >>> Is there any way to share public histories and datasets when galaxy is
> > using external authentication mechanism? I have thought about setting up
> > (fake) anonymous REMOTE_USER variable for /datasets path, but  not sure
> > whether this is correct approach. Also, would it require any galaxy code
> > changes? Any thoughts?
> > >>
> > >> Hi Shantanu,
> > >>
> > >> That's about all you can do, or modify
> > >> lib/galaxy/web/framework/middleware/remoteuser.py to let these
> > >> connections through.  I would suggest the former solution of setting a
> > >> header in Apache, but only set it if the user is not authenticated.
> > >>
> > >> --nate
> > >
> > >
> > > Thanks for the reply Nate. That's helpful.
> > >
> > > --
> > > Shantanu.
> > >
> >
> >
> > I did a test by excluding following URLs from Apache-Shibboleth external
> > authentication and it seems to be working:
> > -  /datasets/
> > -  /u//h/
> > - /static/  (css and javascript)
> >
> > Do I need to exclude any other URLs so that published histories and
> > datasets can be accessed from remote sites without authentication? Also,
> > will it offer read-only access to the galaxy interface? Does it expose any
> > job submission, file-uploads or any other modification/execution operations
> > using web interface?
> >
> > Also, can we prevent particular galaxy-user from carrying out certain
> > actions, e.g. running jobs, file uploads etc.? Since galaxy will create
> > 'anonymous' user account based on the REMOTE_USER variable set for
> > unauthenticated requests, I am wondering if such locked-down mode will be
> > possible for a particular galaxy-user.
> >
> >
> > Thanks,
> > Shantanu.
> >
> >
> >
> >
> > ___
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> > and other Galaxy lists, please use the interface at:
> >
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> >
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Re: [galaxy-dev] User creation with upstream authentication

[Nate Coraor]

Steve Thorn wrote:
> Hi Nate
> 
> Thanks for the reply. Do you have any pointers to how we can achieve 
> authorization in Apache (not my area of experience)? Perhaps you know of 
> other Galaxy groups who do this sort of thing? 

Hi Steve,

Instead of 'Require valid-user' in your Apache config, you can use
either of:

Require user [userid...]

or

Require group [group-name...]

Anyone not listed in the Require directive would be shown a 403 error by
Apache, which you can customize to contain any information necessary to
direct users how to get access (contacting you).

--nate

> 
> Many thanks
> Steve
> 
> 
> On 28 Jun 2011, at 19:31, Nate Coraor wrote:
> 
> > Steve Thorn wrote:
> >> Hello
> >> 
> >> We would like to force users to register even when they successfully
> >> pass through our University's single sign-on service (Apache +
> >> cosign).
> >> 
> >> We have:
> >> 
> >> use_remote_user = True
> >> allow_user_creation = False
> >> 
> >> in the universe_wsgi.ini, but it appears that use_remote_user takes
> >> precedence over allow_user_creation.
> >> 
> >> Ideally, we'd like users who get through the single sign-on to be
> >> presented with a message like "to use galaxy please register by
> >> emailing some...@ed.ac.uk". Is this possible?
> > 
> > Hi Steve,
> > 
> > This is not really possible in Galaxy without some hacking since as you
> > have discovered, remote_user takes precedence over all of the built-in
> > user controls.  You can implement authorization in Apache, though, as a
> > workaround.
> > 
> > --nate
> > 
> >> 
> >> Many thanks,
> >> Steve
> >> -- 
> >> Steve Thorn
> >> Research Systems Consultant - ECDF Middleware Team
> >> +44 (0)131 650 4941
> >> University of Edinburgh, JCMB, King's Buildings
> >> Edinburgh EH9 3JZ, UK
> >> 
> >> The University of Edinburgh is a charitable body, registered in
> >> Scotland, with registration number SC005336.
> >> 
> >> ___
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> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >> 
> >> http://lists.bx.psu.edu/
> > 
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
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Re: [galaxy-dev] Regarding saving the file

[Nate Coraor]

shashi shekhar wrote:
> Hi All,
> 
> 
> 
> Can u tell me how it works?.when u click on save button, it will save a file
> as  output file name appended with extension example
> Galaxy122-[fasta-compute-sequence-length].fasta . i want to remove the first
> word "Galaxy". how it's possible ?

Hi Shashi,

The filename is set on line 373 of
galaxy-dist/lib/galaxy/web/controllers/dataset.py:

367 else:
368 trans.response.headers['Content-Length'] = int( os.stat( 
data.file_name ).st_size )
369 if not to_ext:
370 to_ext = data.extension
371 valid_chars = 
'.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
372 fname = ''.join(c in valid_chars and c or '_' for c in 
data.name)[0:150]
373 trans.response.headers["Content-Disposition"] = 
"attachment; filename=Galaxy%s-[%s].%s" % (data.hid, fname, to_ext)
374 return open( data.file_name )

--nate

> 
> 
> Regards
> shashi shekhar

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Re: [galaxy-dev] changing file storage location

[Sanka, Ravi]

Hi Enis,

No I didn't restart Galaxy after the changes were saved. Is that the process 
explained in the README.txt (setup.sh & run.sh)? That process was for the first 
time, so I didn't repeat it after saving the changes.

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---

From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Wednesday, June 29, 2011 11:32 AM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] changing file storage location

Hi Ravi,
Just a quick check - did you restart Galaxy after saving the changes? What you 
did should direct any new files to the specified location.

Enis
On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi 
mailto:rsa...@jcvi.org>> wrote:
Greetings,

My name is Ravi Sanka. I have a question regarding Galaxy.

Recently, I had a local installation set up and am now trying to change the 
location where the install stores imported and created files.

I opened the config file universe_wsgi.ini and did the following:


-  Removed the '#' mark from '#file_path = database/files'

-  Changed value of file_path to the absolute path of an accessible, 
readable/writable location

-  Saved changes

Despite this, the install still stores files in database/files. Is there a step 
I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again?

I also intend to change the database from the SQLite default to an existing 
database, so I assume the steps to change the file_path also apply to 
database_connection.

Thank you for your time.

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---


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Re: [galaxy-dev] changing file storage location

[Enis Afgan]

In order for Galaxy to acknowledge the changes, you'll have to restart
Galaxy. I'll double check in the wiki to make sure this is stated somewhere
but simply stopping the Galaxy process and starting it back up should reload
the config file.

If your Galaxy is running the background run:
sh run.sh --stop-daemon
sh run.sh --daemon

If the process is not running in the background, simply stop it (i.e., ctrl
+ C)

Enis

On Wed, Jun 29, 2011 at 11:52 AM, Sanka, Ravi  wrote:

> Hi Enis,
>
> ** **
>
> No I didn’t restart Galaxy after the changes were saved. Is that the
> process explained in the README.txt (setup.sh & run.sh)? That process was
> for the first time, so I didn’t repeat it after saving the changes.
>
> ** **
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
> ** **
>
> *From:* Enis Afgan [mailto:eaf...@emory.edu]
> *Sent:* Wednesday, June 29, 2011 11:32 AM
> *To:* Sanka, Ravi
> *Cc:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Re: [galaxy-dev] changing file storage location
>
> ** **
>
> Hi Ravi,
>
> Just a quick check - did you restart Galaxy after saving the changes? What
> you did should direct any new files to the specified location.
>
> ** **
>
> Enis
>
> On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi  wrote:
>
> Greetings,
>
>  
>
> My name is Ravi Sanka. I have a question regarding Galaxy.
>
>  
>
> Recently, I had a local installation set up and am now trying to change the
> location where the install stores imported and created files.
>
>  
>
> I opened the config file universe_wsgi.ini and did the following:
>
>  
>
> -  Removed the ‘#’ mark from ‘#file_path = database/files’
>
> -  Changed value of file_path to the absolute path of an
> accessible, readable/writable location
>
> -  Saved changes
>
>  
>
> Despite this, the install still stores files in database/files. Is there a
> step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be
> run again?
>
>  
>
> I also intend to change the database from the SQLite default to an existing
> database, so I assume the steps to change the file_path also apply to
> database_connection.
>
>  
>
> Thank you for your time.
>
>  
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
>  
>
>
> ___
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> 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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Re: [galaxy-dev] changing file storage location

[Enis Afgan]

Hi Ravi,
Just a quick check - did you restart Galaxy after saving the changes? What
you did should direct any new files to the specified location.

Enis

On Wed, Jun 29, 2011 at 10:43 AM, Sanka, Ravi  wrote:

> Greetings,
>
> ** **
>
> My name is Ravi Sanka. I have a question regarding Galaxy.
>
>  
>
> Recently, I had a local installation set up and am now trying to change the
> location where the install stores imported and created files.
>
> ** **
>
> I opened the config file universe_wsgi.ini and did the following:
>
> ** **
>
> **-  **Removed the ‘#’ mark from ‘#file_path = database/files’
>
> **-  **Changed value of file_path to the absolute path of an
> accessible, readable/writable location
>
> **-  **Saved changes
>
> ** **
>
> Despite this, the install still stores files in database/files. Is there a
> step I’m missing? Does the setup procedure (setup.sh & run.sh) need to be
> run again?
>
> ** **
>
> I also intend to change the database from the SQLite default to an existing
> database, so I assume the steps to change the file_path also apply to
> database_connection.
>
> ** **
>
> Thank you for your time.
>
> ** **
>
> ---
>
> Ravi Sanka
>
> ICS - Bioinformatics Engineer
>
> J. Craig Venter Institute
>
> 301-795-7743
>
> ---
>
> ** **
>
> ___
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> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>
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Re: [galaxy-dev] use remote data without duplication

[Nate Coraor]

Caroline Prenoveau wrote:
> Hi,
> 
> We are a small lab and we would like to use galaxy to do our analysis.
> However we have a very large amount of data that is stored on several
> machines and that we cannot afford to duplicate. Our galaxy server is
> set up on a different machine. We are looking for a way to use our
> remote data inside galaxy without copying it locally. Any ideas/hints?

Hi Caroline,

If your remote data is accessible via the filesystem (i.e. via NFS), you
can "link" it into Galaxy through Data Libraries.  Please see the
documentation on this feature here:


https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

The "Copy data into Galaxy?" checkbox is now a select list (yes/no) and
there are some other minor interface changes, but the rest of the
information is still correct.

--nate

> 
> Thanks,
> 
> Caroline
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[galaxy-dev] changing file storage location

[Sanka, Ravi]

Greetings,

My name is Ravi Sanka. I have a question regarding Galaxy.

Recently, I had a local installation set up and am now trying to change the 
location where the install stores imported and created files.

I opened the config file universe_wsgi.ini and did the following:


-  Removed the '#' mark from '#file_path = database/files'

-  Changed value of file_path to the absolute path of an accessible, 
readable/writable location

-  Saved changes

Despite this, the install still stores files in database/files. Is there a step 
I'm missing? Does the setup procedure (setup.sh & run.sh) need to be run again?

I also intend to change the database from the SQLite default to an existing 
database, so I assume the steps to change the file_path also apply to 
database_connection.

Thank you for your time.

---
Ravi Sanka
ICS - Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
---

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Re: [galaxy-dev] public datasets/histories with external auth

[Leandro Hermida]

Hi Shantanu,

In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path?  I'm just
looking at the Apache docs and the RequestHeader directive has a context of
the entire VirtualHost and cannot be put into a Location container so I'm
not sure how to do it.

thanks,
Leandro

On Wed, Jun 22, 2011 at 9:40 PM, Shantanu Pavgi  wrote:

>
> On Jun 20, 2011, at 4:10 PM, Shantanu Pavgi wrote:
>
> >
> > On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote:
> >
> >> Shantanu Pavgi wrote:
> >>> Hi,
> >>>
> >>> We have a galaxy server setup using external shibboleth authentication.
> While we would like to have site behind authentication realm, there are
> instances when our galaxy datasets/histories need to be accessible publicly
> from other websites. We tried adding an exception to auth rule for /datasets
>  path using Location directive in apache web server configuration, however
> galaxy server returned an error as:
> >>>
> >>> {{{
> >>> Access to Galaxy is denied
> >>> Galaxy is configured to authenticate users via an external method (such
> as HTTP authentication in Apache), but a username was not provided by the
> upstream (proxy) server. This is generally due to a misconfiguration in the
> upstream server.
> >>> }}}
> >>>
> >>> Is there any way to share public histories and datasets when galaxy is
> using external authentication mechanism? I have thought about setting up
> (fake) anonymous REMOTE_USER variable for /datasets path, but  not sure
> whether this is correct approach. Also, would it require any galaxy code
> changes? Any thoughts?
> >>
> >> Hi Shantanu,
> >>
> >> That's about all you can do, or modify
> >> lib/galaxy/web/framework/middleware/remoteuser.py to let these
> >> connections through.  I would suggest the former solution of setting a
> >> header in Apache, but only set it if the user is not authenticated.
> >>
> >> --nate
> >
> >
> > Thanks for the reply Nate. That's helpful.
> >
> > --
> > Shantanu.
> >
>
>
> I did a test by excluding following URLs from Apache-Shibboleth external
> authentication and it seems to be working:
> -  /datasets/
> -  /u//h/
> - /static/  (css and javascript)
>
> Do I need to exclude any other URLs so that published histories and
> datasets can be accessed from remote sites without authentication? Also,
> will it offer read-only access to the galaxy interface? Does it expose any
> job submission, file-uploads or any other modification/execution operations
> using web interface?
>
> Also, can we prevent particular galaxy-user from carrying out certain
> actions, e.g. running jobs, file uploads etc.? Since galaxy will create
> 'anonymous' user account based on the REMOTE_USER variable set for
> unauthenticated requests, I am wondering if such locked-down mode will be
> possible for a particular galaxy-user.
>
>
> Thanks,
> Shantanu.
>
>
>
>
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Re: [galaxy-dev] Refreshing/Reloading Files

[Hans-Rudolf Hotz]

Hi Paul

You probably need to be a bit more specific...at what stage is this 
'.txt file' read (or rather should be read)? - are you offering the 
(growing) list of databases as options to select in the GUI?


Hans


On 06/29/2011 10:20 AM, Admins de Galaxy wrote:

Hello everyone,
we have a problem with one of our selfwritten tools.
We have a tool, that compares sequence with a database.
The List of the available databases is  loaded from a .txt file.

One of our other tools, manages that a new database is
added to the .txt file. But Galaxy doesn't recognize the change.

It would be nice if someone could give us an advice.

Best regards

Paul K. Deuster
@ Technische Hochschule Mittelhessen




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Re: [galaxy-dev] Refreshing/Reloading Files

[Bossers, Alex]

Paul,

as far as I know the config files (probably loc files) are only refreshed on 
galaxy_instance restart unfortunatly.
So when this is possible to do on the fly I am interested as well.

Alex



Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
namens Admins de Galaxy [galaxy.at.thm@googlemail.com]
Verzonden: woensdag 29 juni 2011 10:20
Aan: galaxy-...@bx.psu.edu
Onderwerp: [galaxy-dev] Refreshing/Reloading Files

Hello everyone,
we have a problem with one of our selfwritten tools.
We have a tool, that compares sequence with a database.
The List of the available databases is  loaded from a .txt file.

One of our other tools, manages that a new database is
added to the .txt file. But Galaxy doesn't recognize the change.

It would be nice if someone could give us an advice.

Best regards

Paul K. Deuster
@ Technische Hochschule Mittelhessen


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[galaxy-dev] Refreshing/Reloading Files

[Admins de Galaxy]

Hello everyone,
we have a problem with one of our selfwritten tools.
We have a tool, that compares sequence with a database.
The List of the available databases is  loaded from a .txt file.

One of our other tools, manages that a new database is
added to the .txt file. But Galaxy doesn't recognize the change.

It would be nice if someone could give us an advice.

Best regards

Paul K. Deuster
@ Technische Hochschule Mittelhessen
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Re: [galaxy-dev] Fail to start galaxy

[Hans-Rudolf Hotz]

On 06/28/2011 07:06 PM, colin molter wrote:

hi hans,
you are right.
it seems that even if i stopped galaxy
(i just stopped the run.sh command)

i still have a job running:
root 10441 97.0  0.0  77496  1772 pts/6R11:59 402:48 python
/opt/galaxy-central/tools/fastq/fastq_groomer.py /fs1/GenomicsData/ERP0005

it seems that the transformation of a fastq file is taking a lot of time (it
uses 100%of cpu since 7hours).
does it sound normal?



I am not very familiar with 'fastq_groomer.py' and without knowing the 
size of your fasta file, it is impossible to tell.


Have you tried a subset of your fasta file? May be your data is corrupt 
resulting in an endless loop?



Hans



i think i have better to kill that job and to try another way.

i stopped the job and it works
thx.


2011/6/28 Hans-Rudolf Hotz


Hi Colin


  I launched a big job on my local galaxy server (for which I am admin). The

job was to put local dir in the datalist.
It took too long and i wanted to stop it  but how?? i failed to find a
solution.



go to the admin view ->  'Manage jobs' and there you can kill individual
jobs.


  To stop the job i thought that stopping the galaxy running instance could

make it. (AM I RIGHT?)



possible, but sounds like an 'overkill' to me. I would first try the 'soft'
method described aboveand use this only as a last resort.


  Unfortunately, i failed to restart galaxy. I have the following error:




are you sure you have killed the galaxy process? Since this part of the
error message tells me that Galaxy (or another service) is still using the
port number.



socket.error: (98, 'Address already in use')



How did you stop galaxy?



Regards, Hans






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