[galaxy-dev] Galaxy administrators - admin_users setting
Hi all, To make someone an administrator on a local Galaxy install, do I just need to add their email (login) to the comma separated setting admin_users in universe_wsgi.ini? https://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface I have this working on one server, but it doesn't seem to have any effect on a second server. Both are now running the current release (changeset 50e249442c5a). Is there some other setting needed to enable the admin interface? Thanks, 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] Galaxy administrators - admin_users setting
On Mon, May 9, 2011 at 12:48 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Peter First,the obvious question: Have you restarted galaxy? Yes, and I tried hard reloads in two different browsers (both of which are working on the primary server). Second: I vaguely remember a similar problem, and if I remember correctly, the problem we had was the space between the comma and the next e-mail address. Hence, make sure you write the line like this: admin_users = f...@bar.com,f...@bar.com,f...@bar.com (ie: without any blank spaces) I hope this helps, Hans I'll double check that. As an aside, it would be interesting to check if the comparison is done case insensitively or not (emails and domain names are case insensitive). Fingers crossed... thanks, 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/
[galaxy-dev] External representation of workflow
Hello everyone, I need some advice on how to represent the output of all the different tools inside a workflow in an external application. I am looking into using galaxy as a digital evidence processing tool. It is very important that i can access the intermediate sets of data created by every tool's output. Some have suggested the actual tools should populate a database and that the secondary(viewer) application should just retrieve the applicable data form there. Any suggestions? Any input would be greatly appreciated. Regards Fred ___ 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] [galaxy-user] Megblast GIs
Peter Cock wrote: Which version of BLAST do you have? If you're using the megablast tool in Galaxy, then it will be NCBI legacy BLAST using the blastall binary. If you're using the (commented out by default) BLAST+ wrappers, then it will be using the blastn binary. There were changes to the ID handling in the tabular output in BLAST 2.2.25+ as I recall. Peter, Minor point unrelated to Douglas' original question - the BLAST+ tools are no longer commented in the sample tool config. --nate Another important factor is how the BLAST database was made (with or without the -parse_seqids flag). Peter P.S. Questions like this about local installs might be better on the galaxy-dev list, CC'd. ___ 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] Unable to set metadata in API call
Duddy, John wrote:
I need to be able to set some metadata in some custom data types. For now,
I'm just trying to set the value of the 'misc_info' field. The client script
is this:
put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
'meta data msg' } )
and my API method is as follows. It executes fine, but the values do not show
on the next show() call.
Hi John,
Your method below works fine for existing metadata items like
'data_lines', so I suspect the problem is not with the update method,
but with the datatype definition. Does your class have a 'misc_info'
MetadataElement?
--nate
Disclaimer: Python is still quite new to me, and it's very likely I do not
understand the metadata model and the way library dataset associates work.
Any clues will be greatly appreaciated!
@web.expose_api
def update( self, trans, id, library_id, payload, **kwd ):
PUT
/api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
Sets attributes (metadata) on a library item.
update_type = None
if 'update_type' not in payload:
trans.response.status = 400
return Missing required 'update_type' parameter. Please consult
the API documentation for help.
else:
update_type = payload.pop( 'update_type' )
if update_type not in ( 'metadata' ):
trans.response.status = 400
return Invalid value for 'update_type' parameter ( %s )
specified. Please consult the API documentation for help. % update_type
content_id = id
decoded_type_and_id = trans.security.decode_string_id( content_id )
content_type, decoded_content_id = decoded_type_and_id.split( '.' )
if content_type not in ( 'file' ):
trans.response.status = 400
return Updates allowed only on files, not directories
try:
content = trans.sa_session.query(
trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id )
except:
content = None
if not content or ( not trans.user_is_admin() and not
trans.app.security_agent.can_modify_library_item(
trans.get_current_user_roles(), content, trans.user ) ):
trans.response.status = 400
return Invalid %s id ( %s ) specified. % ( content_type, str(
content_id ) )
metadata = content.get_metadata()
content.datatype.before_setting_metadata(content)
if not metadata:
metadata = {}
for name in payload:
if name not in [ 'name', 'info', 'dbkey' ]:
setattr( metadata, name, payload[name])
content.set_metadata(metadata)
content.datatype.after_setting_metadata( content )
trans.sa_session.flush()
return OK
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
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[galaxy-dev] shared TEMP directory location
I am configuring galaxy to use a shared filesystem location as it's TEMP
directory. I have modified $TEMP variable with the necessary path. Are there
any other changes that I need to make? The cluster config page
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions about
removing or commenting out tool runner configuration, example below:
{{{
[galaxy:tool_runners]
biomart = local:///
encode_db1 = local:///
hbvar = local:///
microbial_import1 = local:///
ucsc_table_direct1 = local:///
ucsc_table_direct_archaea1 = local:///
ucsc_table_direct_test1 = local:///
upload1 = local:///
}}}
Should we replace it with some other value or completely remove it? Also, what
should it be set to for any additional tools that we install?
--
Thanks,
Shantanu.
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Re: [galaxy-dev] Unable to set metadata in API call
Silly me - 'misc_info' shows up in the show() output, but I didn't bother to
verify that it was metadata and not some other member.
Thanks!
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Monday, May 09, 2011 8:27 AM
To: Duddy, John
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Unable to set metadata in API call
Duddy, John wrote:
I need to be able to set some metadata in some custom data types. For now,
I'm just trying to set the value of the 'misc_info' field. The client script
is this:
put( sys.argv[1], sys.argv[2], { 'update_type' : 'metadata', 'misc_info' :
'meta data msg' } )
and my API method is as follows. It executes fine, but the values do not show
on the next show() call.
Hi John,
Your method below works fine for existing metadata items like
'data_lines', so I suspect the problem is not with the update method,
but with the datatype definition. Does your class have a 'misc_info'
MetadataElement?
--nate
Disclaimer: Python is still quite new to me, and it's very likely I do not
understand the metadata model and the way library dataset associates work.
Any clues will be greatly appreaciated!
@web.expose_api
def update( self, trans, id, library_id, payload, **kwd ):
PUT
/api/libraries/{encoded_library_id}/contents/{encoded_content_type_and_id}
Sets attributes (metadata) on a library item.
update_type = None
if 'update_type' not in payload:
trans.response.status = 400
return Missing required 'update_type' parameter. Please consult
the API documentation for help.
else:
update_type = payload.pop( 'update_type' )
if update_type not in ( 'metadata' ):
trans.response.status = 400
return Invalid value for 'update_type' parameter ( %s )
specified. Please consult the API documentation for help. % update_type
content_id = id
decoded_type_and_id = trans.security.decode_string_id( content_id )
content_type, decoded_content_id = decoded_type_and_id.split( '.' )
if content_type not in ( 'file' ):
trans.response.status = 400
return Updates allowed only on files, not directories
try:
content = trans.sa_session.query(
trans.app.model.LibraryDatasetDatasetAssociation ).get( decoded_content_id )
except:
content = None
if not content or ( not trans.user_is_admin() and not
trans.app.security_agent.can_modify_library_item(
trans.get_current_user_roles(), content, trans.user ) ):
trans.response.status = 400
return Invalid %s id ( %s ) specified. % ( content_type, str(
content_id ) )
metadata = content.get_metadata()
content.datatype.before_setting_metadata(content)
if not metadata:
metadata = {}
for name in payload:
if name not in [ 'name', 'info', 'dbkey' ]:
setattr( metadata, name, payload[name])
content.set_metadata(metadata)
content.datatype.after_setting_metadata( content )
trans.sa_session.flush()
return OK
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.commailto:jdu...@illumina.com
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[galaxy-dev] Can I run workflow on certain nodes of the cluster?
Is it possible to run a specific workflow only on certain nodes of the cluster? Either using the API or by setting something in the config files? Thanks, Liisa ___ 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] Dynamically Specifying PBS Resources
Allen, Benjamin S wrote: I'm wondering if its possible to somehow present the user with a param that lets him or her specify number of cores, nodes, memory, and wall time from within the workflow for a specific tool. Other than coming up with a predictive algorithm for each tool's resource needs (memory especially) how is one supposed to efficiently use Galaxy and PBS other than somehow letting the user specify needed resources? Think in cases like assembly, for example with Velvet depending on the input files, resource requirements can be vastly different job to job. Hi Ben, There is not a dynamic method due to the difficulties of predetermining resource requirements based on inputs and parameters (I have never seen this done reliably). A manual method could be feasible for controlled environments, so I've created a feature request for it here: https://bitbucket.org/galaxy/galaxy-central/issue/532/allow-users-to-specify-drm-resource --nate Thanks, Ben ___ 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] Display BAM with IGV
Dave Walton wrote: Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Hi Dave, It's necessary to set up the more advanced configuration under Sending files using nginx on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy? Thanks, --nate Thanks, Dave On 4/27/11 9:07 PM, Dave Walton dave.wal...@jax.org wrote: I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave On 4/27/11 12:33 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see Using a Proxy server at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up. Thanks for using Galaxy, Dan On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote: Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance Alex INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.init(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.init(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length ___ Alexander Graf Laboratory of Functional Genome Analysis Gene Center, University of Munich (LMU) Feodor-Lynen-Strasse 25; 81377 Munich; Germany email: g...@lmb.uni-muenchen.de Internet: www.lafuga.de/genomics.htm http://www.lafuga.de/genomics.htm ___ ___ 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] Can I run workflow on certain nodes of the cluster?
Liisa Koski wrote: Is it possible to run a specific workflow only on certain nodes of the cluster? Either using the API or by setting something in the config files? Hi Liisa, Galaxy currently only allows specification of these sorts of parameters on a per-tool basis, so it's not possible to do it for an entire workflow. I agree this would be a handy feature, but it's unlikely we'd be able to work on it any time soon. --nate Thanks, Liisa ___ 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] problems previewing certain files, downloading files and with login
Matthew Conte wrote: Good afternoon, I'm having several problems with my local galaxy install which may or may not be related to one another. The first problem I'm having is with the Display data in browser feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the Display data in browser eyeball icon. It is simply a blank middle panel. The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download: *This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.* In this case, I don't see anything in the log files either. Hi Matt, Are you using the sendfile/x-accel-redirect configurations of Apache/nginx? Are all of these issues the same if you connect directly to Galaxy's built-in webserver instead of through a proxy server? Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page. For this problem, I do get an error in the galaxy log: *Exception happened during processing of request from * *self.wfile.flush()* * File /raid/galaxy_user/lib/python2.6/socket.py, line 297, in flush* *self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe* I see this occasionally on python 2.6, and it's usually just a harmless intentional interrupted connection. As above, can you test login via the welcome page without the use of the proxy server and report back whether there's any difference? Thanks, --nate I am able to log in via other routes, such as going to Options-Saved Histories which brings up an error You must be logged in to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@umd.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] problems previewing certain files, downloading files and with login
Hi Nate, On Mon, May 9, 2011 at 3:30 PM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: Good afternoon, I'm having several problems with my local galaxy install which may or may not be related to one another. The first problem I'm having is with the Display data in browser feature. Some files type formats (fastqsanger, fasta) display fine. However, other file type formats (png, svg, txt) simply do not display at all. I have debugging turned on, but do not see any error within the browser or within the galaxy log or web server log after clicking the Display data in browser eyeball icon. It is simply a blank middle panel. The next problem I'm having has to do with downloading files. Firefox and Safari will download any file from a history, but will just create an empty file on the client. Again, neither log file show an error with a clue to the problem. Chrome will download some files, but other files give me an error and won't download: *This webpage is not available* * * *error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the connection.* In this case, I don't see anything in the log files either. Hi Matt, Are you using the sendfile/x-accel-redirect configurations of Apache/nginx? Are all of these issues the same if you connect directly to Galaxy's built-in webserver instead of through a proxy server? Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem. Finally, I'm also having a problem logging in from the main welcome page. It seems to authenticate fine (I get an error when I put in the wrong password and don't when I put in the correct password), but it doesn't actually log me in and just takes me back to the main welcome page. For this problem, I do get an error in the galaxy log: *Exception happened during processing of request from * *self.wfile.flush()* * File /raid/galaxy_user/lib/python2.6/socket.py, line 297, in flush* *self._sock.sendall(buffer(data, write_offset, buffer_size))* *error: [Errno 32] Broken pipe* I see this occasionally on python 2.6, and it's usually just a harmless intentional interrupted connection. As above, can you test login via the welcome page without the use of the proxy server and report back whether there's any difference? Thanks, --nate This also works normal with the built-in webserver but not as a proxy server. Thanks, Matt I am able to log in via other routes, such as going to Options-Saved Histories which brings up an error You must be logged in to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@umd.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] problems previewing certain files, downloading files and with login
Matthew Conte wrote: Hi Nate, Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem. Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue. --nate This also works normal with the built-in webserver but not as a proxy server. Thanks, Matt I am able to log in via other routes, such as going to Options-Saved Histories which brings up an error You must be logged in to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@umd.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] problems previewing certain files, downloading files and with login
Hi Nate, I've turned both apache and nginx logging up to debug and still don't see anything of relevance in the error logs for each of the problems I listed. Should I send you my universe_wsgi.ini? Thanks, Matt On Mon, May 9, 2011 at 4:15 PM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: Hi Nate, Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem. Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue. --nate This also works normal with the built-in webserver but not as a proxy server. Thanks, Matt I am able to log in via other routes, such as going to Options-Saved Histories which brings up an error You must be logged in to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@umd.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] problems previewing certain files, downloading files and with login
Matthew Conte wrote: Hi Nate, I've turned both apache and nginx logging up to debug and still don't see anything of relevance in the error logs for each of the problems I listed. Should I send you my universe_wsgi.ini? That'd help, and the relevant sections of your Apache and/or nginx configurations, off-list please. Thanks, --nate Thanks, Matt On Mon, May 9, 2011 at 4:15 PM, Nate Coraor n...@bx.psu.edu wrote: Matthew Conte wrote: Hi Nate, Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx, but both webservers are showing the same problems. If I use Galaxy's built-in webserver, I don't have the above problems, so the problem is probably related to the proxy server. I just can't seem to pinpoint the problem. Okay, thanks for the info. Have you enabled debug logging in the proxy and checked the error logs for anything telling? Same for the login issue. --nate This also works normal with the built-in webserver but not as a proxy server. Thanks, Matt I am able to log in via other routes, such as going to Options-Saved Histories which brings up an error You must be logged in to work with multiple histories and links to /galaxy/user/login?webapp=galaxy and from there I can log in fine. This happens with both admin and normal users. It is not a huge problem since I have a work around, but it would be nice to figure out the problem so I don't have to make my users do the same. I should mention that I'm running galaxy-dist changeset 50e249442c5a on CentOS. The problems seem to be web server independent too as they appear with both Apache and Nginx. I've used the following instructions, but I'm just not seeing where the problem(s) is/are: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling Thanks, Matt -- Matthew Conte Bioinformatics Scientist Department of Biology University of Maryland mco...@umd.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/
