[galaxy-dev] Requests to display_application mistakenly routed to route
Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through display_application. When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam --2012-06-22 13:58:00-- http://example.org /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.org:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.org /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf Reusing existing connection to example.org:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ = ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University ___ 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] Requests to display_application mistakenly routed to route
Sorry, the subject should read mistakenly routed to root. The question still stands. -r On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme rob.s...@gmail.com wrote: Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through display_application. When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam --2012-06-22 13:58:00-- http://example.org /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.org:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.org /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf Reusing existing connection to example.org:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ = ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University ___ 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] Requests to display_application mistakenly routed to route
The problem seems to be in the lack of authentication by the request sent by IGV. The galaxy instance is set to require a username and password with require_login = True in universe_wsgi.ini, which means that when IGV attempts to download the BAM file at http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default//data/galaxy_e2132aef71b11dbf.bam, galaxy redirects to the login page. I tried to remove the authentication requiements with the apache config (as per https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy ): LocationMatch display_application/[a-zA-Z0-9]+/igv.* RequestHeader set REMOTE_USER igv_disp...@example.org Satisfy Any Order deny,allow Allow from all /LocationMatch But it didn't help. Commenting out the require_login = True line allows IGV to connect and download the bam file without issue. I've now got IGV crashing when trying to access this BAM file, but that's probably a question for their list. -r On Fri, Jun 22, 2012 at 2:16 PM, Rob Syme rob.s...@gmail.com wrote: Sorry, the subject should read mistakenly routed to root. The question still stands. -r On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme rob.s...@gmail.com wrote: Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through display_application. When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam --2012-06-22 13:58:00-- http://example.org /galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.org:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.org /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf Reusing existing connection to example.org:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ = ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University ___ 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] Local jobs aren't dispatching in a balanced configuration deployed on a cluster
On Jun 21, 2012, at 4:50 PM, Dorset, Daniel C wrote: I have galaxy running on my institution’s cluster computing service, which uses PBS. It’s in a balanced configuration. Jobs going to the cluster submit without any problem at all. However, any job that I have specified to run locally in the universe_wgsi.ini file won’t dispatch. There isn’t any record of the job in the manager.log, or any of the handler[#].log files. In fact, I’ve never seen anything in the handler logfiles after “serving on [GALAXY IP]:[SPECIFIC PORT NUMBER OF HANDLER]”. The manager logfile has all the details about the jobs dispatched to the pbs runner, but nothing about local jobs. HOWEVER, if I stop Galaxy using “GALAXY_RUN_ALL=1 sh ./run.sh --stop-daemon” and restart using “GALAXY_RUN_ALL=1 sh ./run.sh --daemon” then the local jobs that were waiting to run begin immediately. Information about them shows up in manager.log, but not in the handler0.log or handler1.log files. I’m on an 8-core Dell R410 server, if that matters. The server portion of my universe_wsgi.ini file is pasted below. # HTTP Server -- # Configuration of the internal HTTP server. [server:web0] # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. port = 8080 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = localhost # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 7 [server:web1] use = egg:Paste#http port = 8081 host = localhost use_threadpool = true threadpool_workers = 7 [server:manager] use = egg:Paste#http port = 8079 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8090 host = localhost use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = localhost use_threadpool = true threadpool_workers = 5 [app:main] # -- Application and filtering job_manager = manager job_handler = handler0,handler1 Hi Daniel, This parameter should be 'job_handlers' Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections? --nate # Custom Parameters ___ 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] Requests to display_application mistakenly routed to route
While I have not yet added IGV for display, I would like to and I would also like to add tablet so I'm interested in how this plays out. Hopefully someone more knowledgable will chime in. Meanwhile, I'll try to help. I think that the 302 redirect indicates that REMOTE_USER is not being set or is not beiing respected. I think you have to enable external authentication in universe_wsgi.ini for REMOTE_USER to be respected by galaxy. Assuming you do have external auth set up... Can you actually log in to galaxy as igv_disp...@example.orgmailto:igv_disp...@example.org? I think you would need to either configure that user in galaxy or allow it to be automatically created (via allow_user_creation) It might also be worth looking at remote_user_maildomain and try eliminating the @example.org Another possibility: are you sure that this url http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default//data/galaxy_e2132aef71b11dbf.bam... is matched by LocationMatch display_application/[a-zA-Z0-9]+/igv.* I don't know if a regex in a LocationMatch is implicitly left anchored. might be worth trying /galaxy/display_application/... Brad On Jun 22, 2012, at 3:48 AM, Rob Syme wrote: The problem seems to be in the lack of authentication by the request sent by IGV. The galaxy instance is set to require a username and password with require_login = True in universe_wsgi.ini, which means that when IGV attempts to download the BAM file at http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default//data/galaxy_e2132aef71b11dbf.bam, galaxy redirects to the login page. I tried to remove the authentication requiements with the apache config (as per https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy): LocationMatch display_application/[a-zA-Z0-9]+/igv.* RequestHeader set REMOTE_USER igv_disp...@example.orgmailto:igv_disp...@example.org Satisfy Any Order deny,allow Allow from all /LocationMatch But it didn't help. Commenting out the require_login = True line allows IGV to connect and download the bam file without issue. I've now got IGV crashing when trying to access this BAM file, but that's probably a question for their list. -r On Fri, Jun 22, 2012 at 2:16 PM, Rob Syme rob.s...@gmail.commailto:rob.s...@gmail.com wrote: Sorry, the subject should read mistakenly routed to root. The question still stands. -r On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme rob.s...@gmail.commailto:rob.s...@gmail.com wrote: Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through display_application. When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam --2012-06-22 13:58:00-- http://example.orghttp://example.org//galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.orghttp://example.org/:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.orghttp://example.org//galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf Reusing existing connection to example.orghttp://example.org/:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ = ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University ___ 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/ -- Brad Langhorst langho...@neb.commailto:langho...@neb.com
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote: I have recently performed a fresh installation of Galaxy utilizing the latest distribution and am getting a sizable number of errors when attempting to start the server. The issue started when I performed a merge so I decided to do the clean install as a test. The server appears to start just fine, but with errors reported in the logs. The web0.log gives the following errors and warnings (I am truncating the file for space): galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97 galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools version 2 galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg successfully loaded for postgres dialect galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded reference to tool shed: Galaxy test tool shed galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding conflicting datatype with extension 'coverage', using datatype from datatypes_conf.xml. galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for datatype 'galaxy.datatypes.xml:BlastXml' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table 'bfast_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table 'blastdb_p' galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2012-06-20 18:29:21,066 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG
Re: [galaxy-dev] Local jobs aren't dispatching in a balanced configuration deployed on a cluster
Good catch, thanks Nate! I have plenty of tool_runners defined, but no tool_handlers. Do I have to specifically assign tool handlers in order for them to be used in job deployment? Thanks! Dan Hi Daniel, This parameter should be 'job_handlers' Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections? --nate ___ 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] Local jobs aren't dispatching in a balanced configuration deployed on a cluster
On Jun 22, 2012, at 12:26 PM, Dorset, Daniel C wrote: Good catch, thanks Nate! I have plenty of tool_runners defined, but no tool_handlers. Do I have to specifically assign tool handlers in order for them to be used in job deployment? No, if you don't define any specific handlers in the [galaxy:tool_handlers], each job will have one assigned randomly from the list in the 'job_handers' parameter in [app:main]. --nate Thanks! Dan Hi Daniel, This parameter should be 'job_handlers' Are there any entries in your [galaxy:tool_handlers] and/or [galaxy:tool_runners] sections? --nate ___ 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] tool_conf.xml and toolbar ordering
Hi Robert, This section of the tool shed wiki should provide the information you need. http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel Greg Von Kuster On Jun 21, 2012, at 5:33 PM, Robert Chase wrote: Hello, We are trying to perfect some of the details of our tool bar. Some new sections we created and added to the beginning of the tool_conf.xml file appear at the bottom of the tool bar. Do we have to do something to get galaxy to reload the tool bar from scratch? -Rob ___ 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] Requests to display_application mistakenly routed to route
Hi Rob, Changeset 7300:f197c4346cc4, which is currently available in galaxy-central, should allow the external display applications to work when require_login = True, thanks for reporting this error. Please let us know if you encounter additional issues. Thanks for using Galaxy, Dan On Jun 22, 2012, at 3:48 AM, Rob Syme wrote: The problem seems to be in the lack of authentication by the request sent by IGV. The galaxy instance is set to require a username and password with require_login = True in universe_wsgi.ini, which means that when IGV attempts to download the BAM file at http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default//data/galaxy_e2132aef71b11dbf.bam, galaxy redirects to the login page. I tried to remove the authentication requiements with the apache config (as per https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy): LocationMatch display_application/[a-zA-Z0-9]+/igv.* RequestHeader set REMOTE_USER igv_disp...@example.org Satisfy Any Order deny,allow Allow from all /LocationMatch But it didn't help. Commenting out the require_login = True line allows IGV to connect and download the bam file without issue. I've now got IGV crashing when trying to access this BAM file, but that's probably a question for their list. -r On Fri, Jun 22, 2012 at 2:16 PM, Rob Syme rob.s...@gmail.com wrote: Sorry, the subject should read mistakenly routed to root. The question still stands. -r On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme rob.s...@gmail.com wrote: Galaxy type: local I'm trying to get IGV to download files served from the galaxy instance through display_application. When IGV makes a request for the BAM file, it is re-routed to root like so: wget http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam --2012-06-22 13:58:00-- http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam Connecting to example.org:80... connected. HTTP request sent, awaiting response... 302 Found Location: /galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf [following] --2012-06-22 13:58:00-- http://example.org/galaxy/root?app_action=datauser_id=cc7ba224ab9e7b70app_name=igv_bamlink_name=local_defaultaction_param=galaxy_e2132aef71b11dbf.bamdataset_id=e2132aef71b11dbf Reusing existing connection to example.org:80. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/html] Saving to: 'galaxy_e2132aef71b11dbf.bam.1' [ = ] 27,581 --.-K/s in 0s 2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581] Giving us a text/html page rather than the BAM file. I see that I'm not the first person to run into this: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm still not really sure how to solve the problem. I'm no sysadmin, so my apache config skills are very patchy. My config is up at https://gist.github.com/2970592. Any help would be very much appreciated. Rob Syme PhD Student Curtin University ___ 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] tool_data_table_config.xml.sample
Hello Birgit, I've committed a fix for this is change set 7302:c4f325ba7caa, which is available in the Galaxy central repository, and is running on both Galaxy tool sheds. I've made sure that your cg_cgatools_linux repository is now functional. Thanks very much for finding this additional issue, and for your patience in resolving these problems. Hopefully things will be smoother from here on for you, but please let me know if you do encounter additional problems. There are many complexities in making the various tools work as expected in the tool shed, so issues like this tend to crop up every so often. Thanks again, Greg Von Kuster On Jun 20, 2012, at 11:41 AM, Birgit Crain wrote: I have to refine that statement about the error message I'm getting now: On upload I get the same error message Metadata was defined for some items in revision 'e183f52194a5'. Correct the following problems if necessary and reset metadata. join.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. junctiondiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. listtestvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. listvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. snpdiff.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. testvariants.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. varfilter.xml - This file refers to a missing file cg_crr_files.loc. Upload a file named cg_crr_files.loc.sample to the repository to correct this error. One tool (calldiff.xml) shows as valid tool, but clicking on that tool I get the message: In green box: Error loading tool: [Errno 2] No such file or directory: '/var/opt/galaxy/g2cmnty/galaxy_toolshed/shed-tool-data/cg_crr_files.loc'. Below that: Tool not properly loaded. The tools displayed as invalid tools just show the 'Tool not properly loaded' message. This is what I got in the main toolshed. I went back to the test toolshed and uploaded the same tar ball there, none of the tools loaded properly. Hope this helps. Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Birgit Crain bcr...@completegenomics.com Date: Tuesday, June 19, 2012 8:25 AM To: Greg Von Kuster g...@bx.psu.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample Same file structure, but updated files and added the executable and tool_config.xml.sample for users who install manually. Here's the tar ball. Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Greg Von Kuster g...@bx.psu.edu Date: Monday, June 18, 2012 5:29 PM To: Birgit Crain bcr...@completegenomics.com Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample Hi Birgit, Did you upload the same tarball you sent me previously, or was it a different tarball. If different, can you send it to me? Thanks On Jun 18, 2012, at 8:18 PM, Birgit Crain wrote: Hi Greg I just created a repository on the main toolshed and upload a tar ball. I got the same error messages again as described in the email thread below. Regards Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete Genomics, Inc. (650) 428-6023 office | (408) 605-3938 mobile bcr...@completegenomics.com From: Greg Von Kuster g...@bx.psu.edu Date: Thursday, June 14, 2012 11:44 AM To: Birgit Crain bcr...@completegenomics.com Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_data_table_config.xml.sample Hello Birgit, This issue has been resolved in changeset 7272:b761471d7590, which is currently available from our Galaxy central repository. Both the Galaxy test and Galaxy main tool sheds are running this latest changeset revision. Thanks very much for reporting this problem! Greg Von Kuster On Jun 14, 2012, at 12:45 PM, Birgit Crain wrote: Hi Greg I was using the Galaxy test toolshed to upload the files into a repository. On my Mac where I develop the tools I have a local instance that I loaded from zipped file (downloaded April
[galaxy-dev] FastQC Tool Errors
Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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] FastQC Tool Errors
Do you run an X11 virtual frame buffer - eg Xvfb? Otherwise AFAIK R graphics and Java will complain on headless nodes. On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: Exception in thread main java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.init(Window.java:437) at java.awt.Frame.init(Frame.java:419) at java.awt.Frame.init(Frame.java:384) at javax.swing.JFrame.init(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.init(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102) Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
