[galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners
Hi all. When I run the FastQC tool using the default local job runner, it produces a folder of files with permission 664: snip -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 error.png -rw-rw-r-- 1 galaxy galaxy 7.5K Jul 5 17:29 fastqc_data.txt snip When I switch to using the(local) pbs queue, it produces a folder with permissions 600: snip -rw--- 1 galaxy galaxy 15K Jul 6 09:10 duplication_levels.png -rw--- 1 galaxy galaxy 1.6K Jul 6 09:10 error.png -rw--- 1 galaxy galaxy 8.8K Jul 6 09:10 fastqc_data.txt snip The final dat file (in database/files/000/dataset_xx.dat) is fine, it's just the files in the corresponding folder (database/files/000/dataset_xx_files/*) that have the incorrect permissions. These more restrictive permissions mean that the files cannot be read by apache, resulting a bunch of broken links when viewing the tool's output. Does anybody know why this might be happening or how to resolve it? Many thanks. -r ___ 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] 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/
