Re: [galaxy-dev] Fail to start galaxy
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 Hotzh...@fmi.ch 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 ___ 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/
[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 ___ 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/
Re: [galaxy-dev] Refreshing/Reloading Files
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 ___ 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/
Re: [galaxy-dev] Refreshing/Reloading Files
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 ___ 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/ ___ 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/
Re: [galaxy-dev] public datasets/histories with external auth
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 pa...@uab.edu 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/username/h/history-name
- /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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[galaxy-dev] changing file storage location
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/
Re: [galaxy-dev] use remote data without duplication
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 ___ 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/ ___ 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/
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 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 --- ** ** ___ 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/ ___ 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/
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 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 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 --- ___ 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/ ** ** ___ 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/
Re: [galaxy-dev] changing file storage location
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 rsa...@jcvi.orgmailto: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 301-795-7743tel: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/ ___ 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/
Re: [galaxy-dev] Regarding saving the file
shashi shekhar wrote:
Hi All,
a href=${h.url_for( controller='dataset', action='display',
dataset_id=dataset_id, to_ext=data.ext )} title=Save class=icon-button
disk tooltip/a
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] User creation with upstream authentication
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. ___ 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/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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/
Re: [galaxy-dev] public datasets/histories with external auth
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 pa...@uab.edu 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/username/h/history-name
- /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] bwa failure preparing job
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: !--options from_data_table=bowtie_indexes/-- 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 ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] changing file storage location
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:///db_name?user=user_namepassword=your_pass 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 rsa...@jcvi.orgmailto: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 301-795-7743tel:301-795-7743 --- From: Enis Afgan [mailto:eaf...@emory.edumailto:eaf...@emory.edu] Sent: Wednesday, June 29, 2011 11:32 AM To: Sanka, Ravi Cc: galaxy-dev@lists.bx.psu.edumailto: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 rsa...@jcvi.orgmailto: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 301-795-7743tel: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/ ___ 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/
Re: [galaxy-dev] changing file storage location
Almost, mysql requires two forward slashes, like so: database_connection = mysql://galaxy:password_here@ host/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 rsa...@jcvi.org 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:///db_name?user=user_namepassword=your_pass ** ** 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 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 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 --- ___ 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/ ** ** ___ 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/
Re: [galaxy-dev] Question about installing NCBI BLAST+ onto Galaxy
On Tue, Jun 28, 2011 at 9:52 PM, George Michopoulos gior...@stanford.edu 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 ___ 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/
Re: [galaxy-dev] public datasets/histories with external auth
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
Directory, Location, Files, and Proxy 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.
Location ~ /(datasets|history)/
AuthType shibboleth
ShibRequireSession off
Require shibboleth
RewriteCond %{LA-U:REMOTE_USER} =
RequestHeader set REMOTE_USER anonymous
/Location
Hope this helps.
1. http://httpd.apache.org/docs/current/mod/directive-dict.html#Context
--
Shantanu.
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Re: [galaxy-dev] public datasets/histories with external auth
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/username/h/history-name - /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_timeoperation=Viewid=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%25sdisplay_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.domainmailto:'anonymous@mail.domain'. Now we are opening up certain URL patterns to be accessed as 'anonymous@mail.domainmailto:'anonymous@mail.domain' user. These URL patterns include following formats as mentioned - /datasets, /history, /u/username/hhistory-name, 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. ___ 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/
