Re: [galaxy-dev] Requests to display_application mistakenly routed to route
Hi Rob,
Thanks for the suggestion, a similar change has just been added in changeset
7306:319b2b0e832c.
Thanks for using Galaxy,
Dan
On Jun 23, 2012, at 1:09 AM, Rob Syme wrote:
Thanks Dan. I'll pull in the change on Monday (don't have access to our
instance atm).
On a related note which might be of interest to Brad, can I suggest that
$GALAXY_ROOT/display_applications/igv/[bam/sam].xml include:
amp;name=${bam_file.name}
at the the end of the url generated for IGV viewing. At the moment, pulling
down galaxy bam files generates uninformative track names. Adding the 'name'
parameter to the url will copy the name of the dataset in galaxy to the name
of the track. If you're pulling in many bam tracks into IGV, this tiny change
makes everything a *lot* easier.
See http://youtu.be/88MKSHHYHjc for an example.
Thanks for the great work, Galaxy devs.
-r
On Sat, Jun 23, 2012 at 1:32 AM, Daniel Blankenberg d...@bx.psu.edu wrote:
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
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[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] 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] 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/
