Alessandro Rossoni | 21 Oct 20:56 2014
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/cgi-bin/ issue - Ubuntu

Dear GBrowse support team,
After some days of struggle and searching the internet, I am writing to you about my problem while trying to get GBrowse2 working properly.

I have tried installing GBrowse on Ubuntu 12.04 and 14.04. In both cases I encountered the same issue. I always get the following message:

"The requested URL /cgi-bin/gbrowse2/gbrowse/volvox was not found on this server." (404 Not Found)
or
"The requested URL /cgi-bin/gb2/gbrowse/yeast was not found on this server." (404 Not Found)

However, when a collegue of mine tried to install GBrowse2 on Debian (following the same installation procedure as described in the HOWTOS) everything instantly works. Unfortunately our server works with Ubuntu.

I also attached the apache2 error log, although today (10/21) no new error was reported (and I experimented a lot)

Thanks in advance for your help.
Alessandro Rossoni


Plant Biochemisty, AG Weber
Heinrich Heine Universitaet Duesseldorf
Germany
[Mon Oct 20 23:22:28.836764 2014] [mpm_event:notice] [pid 7357:tid 140029404981120] AH00489:
Apache/2.4.7 (Ubuntu) configured -- resuming normal operations
[Mon Oct 20 23:22:28.836843 2014] [core:notice] [pid 7357:tid 140029404981120] AH00094: Command line: '/usr/sbin/apache2'
[Mon Oct 20 23:22:31.001742 2014] [mpm_event:notice] [pid 7357:tid 140029404981120] AH00491: caught
SIGTERM, shutting down
[Mon Oct 20 23:22:32.049489 2014] [mpm_event:notice] [pid 7517:tid 140449131902848] AH00489:
Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 configured -- resuming normal operations
[Mon Oct 20 23:22:32.049561 2014] [core:notice] [pid 7517:tid 140449131902848] AH00094: Command line: '/usr/sbin/apache2'
[Mon Oct 20 23:26:26.357920 2014] [mpm_event:notice] [pid 7517:tid 140449131902848] AH00491: caught
SIGTERM, shutting down
[Mon Oct 20 23:26:27.405138 2014] [mpm_event:notice] [pid 12646:tid 140356297430912] AH00489:
Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 configured -- resuming normal operations
[Mon Oct 20 23:26:27.405213 2014] [core:notice] [pid 12646:tid 140356297430912] AH00094: Command
line: '/usr/sbin/apache2'
[Mon Oct 20 23:58:23.500514 2014] [mpm_event:notice] [pid 12646:tid 140356297430912] AH00494: SIGHUP
received.  Attempting to restart
[Mon Oct 20 23:58:23.552022 2014] [mpm_event:notice] [pid 12646:tid 140356297430912] AH00489:
Apache/2.4.7 (Ubuntu) mod_fcgid/2.3.9 configured -- resuming normal operations
[Mon Oct 20 23:58:23.552041 2014] [core:notice] [pid 12646:tid 140356297430912] AH00094: Command
line: '/usr/sbin/apache2'
127.0.0.1 - - [20/Oct/2014:23:29:39 +0200] "GET /gbrowse2 HTTP/1.1" 301 570 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:40 +0200] "GET /gbrowse2/ HTTP/1.1" 200 1822 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:40 +0200] "GET /gbrowse2/tutorial/tutorial.css HTTP/1.1" 200 622
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:40 +0200] "GET /gbrowse2/gmod_cog.jpeg HTTP/1.1" 200 5575
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:41 +0200] "GET /favicon.ico HTTP/1.1" 404 498 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:41 +0200] "GET /favicon.ico HTTP/1.1" 404 498 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:48 +0200] "GET /gb2/gbrowse/yeast HTTP/1.1" 404 505
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/tutorial.html HTTP/1.1" 200
51481 "http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0)
Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/basics1.gif HTTP/1.1"
200 64365 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/basic_conf1.gif
HTTP/1.1" 200 4330 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/basic_conf2.gif
HTTP/1.1" 200 4123 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/descriptions1.gif
HTTP/1.1" 200 7960 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/aliases.gif HTTP/1.1"
200 50078 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/segmented_features2.gif HTTP/1.1" 200 13186
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/canonical_gene1.gif
HTTP/1.1" 200 6165 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/canonical_gene3.gif
HTTP/1.1" 200 5169 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/custom_aggregators1.gif HTTP/1.1" 200 5000
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/cds1.gif HTTP/1.1" 200
11260 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/graph1.gif HTTP/1.1"
200 10949 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/predicted_genes.gif
HTTP/1.1" 200 6493 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/wiggle_density.png
HTTP/1.1" 200 11101 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/dna1.png HTTP/1.1" 200
17911 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/dna2.png HTTP/1.1" 200
20087 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments1.gif HTTP/1.1" 200 7837
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments2.gif HTTP/1.1" 200 7914
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments3.gif HTTP/1.1" 200 4067
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET
/gbrowse2/tutorial/figures/adding_dna_to_alignments1.gif HTTP/1.1" 200 22569
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/trace1.png HTTP/1.1"
200 7192 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/trace2.png HTTP/1.1"
200 8352 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/overview1.gif
HTTP/1.1" 200 16371 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/semantic_zooming1.gif
HTTP/1.1" 200 3065 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/enhancements3.gif
HTTP/1.1" 200 11597 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/categorytable.png
HTTP/1.1" 200 9592 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/plugins1.gif HTTP/1.1"
200 14619 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/plugins2.gif HTTP/1.1"
200 7987 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/third_party2.gif
HTTP/1.1" 200 34452 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/third_party1.gif
HTTP/1.1" 200 226054 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/setting_popup.png
HTTP/1.1" 200 26457 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/tutorial/figures/config_editing.png
HTTP/1.1" 200 40408 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:29:56 +0200] "GET /gbrowse2/images/buttons/share.png HTTP/1.1" 200
450 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:30:19 +0200] "GET /cgi-bin/gbrowse2/gbrowse/volvox HTTP/1.1" 404 519
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:31:30 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:32:04 +0200] "GET / HTTP/1.1" 200 3594 "-" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:32:04 +0200] "GET /icons/ubuntu-logo.png HTTP/1.1" 200 3688
"http://127.0.1.1/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:32:06 +0200] "GET /favicon.ico HTTP/1.1" 404 498 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:32:06 +0200] "GET /favicon.ico HTTP/1.1" 404 498 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:58:40 +0200] "GET /server-status HTTP/1.0" 200 3566 "-"
"Lynx/2.8.8pre.4 libwww-FM/2.14 SSL-MM/1.4.1 GNUTLS/2.12.23"
127.0.0.1 - - [20/Oct/2014:23:59:28 +0200] "GET / HTTP/1.1" 200 3594 "-" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:59:29 +0200] "GET /icons/ubuntu-logo.png HTTP/1.1" 200 3688
"http://localhost/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [20/Oct/2014:23:59:30 +0200] "GET /favicon.ico HTTP/1.1" 404 498 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:00:49 +0200] "GET /gbrowse2/ HTTP/1.1" 200 1823 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:00:50 +0200] "GET /gbrowse2/tutorial/tutorial.css HTTP/1.1" 200 622
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:00:50 +0200] "GET /gbrowse2/gmod_cog.jpeg HTTP/1.1" 304 180
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:00:56 +0200] "GET /gbrowse2/example_scripts HTTP/1.1" 301 602
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:00:56 +0200] "GET /gbrowse2/example_scripts/ HTTP/1.1" 200 782
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:00:01:15 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:20 +0200] "GET /favicon.ico HTTP/1.1" 404 499 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/tutorial.html HTTP/1.1" 200
51481 "http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0)
Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/tutorial.css HTTP/1.1" 200 622
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/basics1.gif HTTP/1.1"
304 180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/basic_conf1.gif
HTTP/1.1" 304 179 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/basic_conf2.gif
HTTP/1.1" 304 180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/descriptions1.gif
HTTP/1.1" 304 181 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/aliases.gif HTTP/1.1"
304 180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET
/gbrowse2/tutorial/figures/segmented_features2.gif HTTP/1.1" 304 180
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/canonical_gene3.gif
HTTP/1.1" 304 180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/canonical_gene1.gif
HTTP/1.1" 304 181 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/predicted_genes.gif
HTTP/1.1" 304 180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:09:24:35 +0200] "GET /gbrowse2/tutorial/figures/cds1.gif HTTP/1.1" 304
180 "http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
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rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:19:17:34 +0200] "GET
/gbrowse2/tutorial/data_files/volvox_remarks.gff3 HTTP/1.1" 200 1165
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:19:26:07 +0200] "GET /cgi-bin/gb2/gbrowse/volvox HTTP/1.1" 404 514
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:19:31:13 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:19:32:06 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:19:40:40 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
134.99.200.87 - - [21/Oct/2014:20:02:46 +0200] "GET /gbrowse2/ HTTP/1.1" 200 1823 "-" "Mozilla/5.0
(X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:46 +0200] "GET /gbrowse2/tutorial/tutorial.css HTTP/1.1" 200
622 "http://134.99.200.47/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0)
Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:46 +0200] "GET /gbrowse2/gmod_cog.jpeg HTTP/1.1" 200 5576
"http://134.99.200.47/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0)
Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:46 +0200] "GET /favicon.ico HTTP/1.1" 404 502 "-" "Mozilla/5.0
(X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:47 +0200] "GET /favicon.ico HTTP/1.1" 404 502 "-" "Mozilla/5.0
(X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/tutorial.html HTTP/1.1" 200
51480 "http://134.99.200.47/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0)
Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/basics1.gif
HTTP/1.1" 200 64365 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/basic_conf1.gif
HTTP/1.1" 200 4330 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/basic_conf2.gif
HTTP/1.1" 200 4122 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/aliases.gif
HTTP/1.1" 200 50078 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/descriptions1.gif
HTTP/1.1" 200 7961 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/canonical_gene1.gif HTTP/1.1" 200 6165
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/segmented_features2.gif HTTP/1.1" 200 13186
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/canonical_gene3.gif HTTP/1.1" 200 5168
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/predicted_genes.gif HTTP/1.1" 200 6493
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/cds1.gif HTTP/1.1"
200 11260 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/custom_aggregators1.gif HTTP/1.1" 200 5000
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/graph1.gif
HTTP/1.1" 200 10949 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/wiggle_density.png HTTP/1.1" 200 11101
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/dna1.png HTTP/1.1"
200 17911 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/dna2.png HTTP/1.1"
200 20087 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments1.gif HTTP/1.1" 200 7837
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments2.gif HTTP/1.1" 200 7914
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/multiple_alignments3.gif HTTP/1.1" 200 4067
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/adding_dna_to_alignments1.gif HTTP/1.1" 200 22569
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/trace1.png
HTTP/1.1" 200 7192 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/trace2.png
HTTP/1.1" 200 8352 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/overview1.gif
HTTP/1.1" 200 16371 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/semantic_zooming1.gif HTTP/1.1" 200 3065
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/enhancements3.gif
HTTP/1.1" 200 11597 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/categorytable.png
HTTP/1.1" 200 9592 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/plugins1.gif
HTTP/1.1" 200 14619 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/plugins2.gif
HTTP/1.1" 200 7987 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/third_party2.gif
HTTP/1.1" 200 34452 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/setting_popup.png
HTTP/1.1" 200 26457 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET
/gbrowse2/tutorial/figures/config_editing.png HTTP/1.1" 200 40408
"http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/images/buttons/share.png HTTP/1.1"
200 450 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
134.99.200.87 - - [21/Oct/2014:20:02:48 +0200] "GET /gbrowse2/tutorial/figures/third_party1.gif
HTTP/1.1" 200 226054 "http://134.99.200.47/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
127.0.0.1 - - [21/Oct/2014:20:29:55 +0200] "GET /favicon.ico HTTP/1.1" 404 499 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:20:30:09 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:20:40:02 +0200] "GET /favicon.ico HTTP/1.1" 404 499 "-" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:20:40:14 +0200] "GET /cgi-bin/gbrowse2/gbrowse/volvox HTTP/1.1" 404 519
"http://localhost/gbrowse2/tutorial/tutorial.html" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:33.0) Gecko/20100101 Firefox/33.0"
127.0.0.1 - - [21/Oct/2014:20:42:14 +0200] "GET /cgi-bin/gb2/gbrowse/yeast HTTP/1.1" 404 513
"http://localhost/gbrowse2/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:33.0) Gecko/20100101 Firefox/33.0"
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John Portwood | 20 Oct 21:21 2014
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Re: vista_plot glyph fails to load

I've resolved the issue now. Turns out I did not have Bio::DB::BigFile
properly installed. Compiling the vista_plot file individually with "perl -c
vista_plot.pm" spat out a more informative error.

Thanks!

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/vista-plot-glyph-fails-to-load-tp5712800p5712837.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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Lau, Branden M - (bmlau | 20 Oct 19:16 2014
Picon

GFF3 editor?

Hi,

I was wondering if there was any program or tool that can edit a GFF3 file that's not a perl script? For example I have a file where I need to edit the first column in order to append information. 

Thanks,
Branden
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Jeff Nie | 20 Oct 05:21 2014
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heat map glyph

Hi,  
I am trying to display 50 gene level RNA-SEQ expression value (percentile) with subtrack and heat map glyph. I chose track space as compact, but one subtrack always show in two or three lines instead of one line. Any idea why? 
data is loaded to mysql db. The related config file look like this:
########
feature  = RNA-Seq
glyph    = heat_map
start_color = white
end_color   = black
min_score   = 0
max_score   = 100
category = RNA-Seq
bump = 1
key         = RNA-Seq Percentiled Gene Expression
subtrack select = Sample source
subtrack table  =  control 1;
                   control 2;
                   case1;
                   case2;
                   ......

Thanks,
Jeff 








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krkerwin | 14 Oct 06:47 2014
Picon
Picon

using ybrowse

Thomas:

 

I just sent Astrid an email regarding ybrowse when I found this email address at the bottom of the webpage.  I was able to download the Variant Frequency by Haplogroup and now need to get the info below to submit our CTS4466 SNPs to ISOGG

 

I need to use ybrowse to find the following for example.  I’ve used the previous database when my family took the WTY test but have since forgotten the details.

 

Name:

CTS11338

Type:

snp

Source:

point

Position:

ChrY:23075481..23075481 (+ strand)

Length:

1

ISOGG_haplogroup:

not listed

YCC_haplogroup:

Aprrox. hg: I

allele_anc:

C

allele_der:

T

comments:

Syn. with CTS10400

count_derived:

0

count_tested:

4

mutation:

C to T

primer_f:

CTS11338_F TGACAGGGGGATGCTTATTG

primer_r:

CTS11338_R GTGTTCCATCAGCCTGTGAG

ref:

Chris Tyler-Smith (2011)

primary_id:

81101

gbrowse_dbid:

chrY:database

 

Thank you very much in advance.  We have quite a few SNPs to submit thanks to you and Astrid.

 

Apparently ISOGG is starting almost from scratch for the R Haplogroup which I believe is likely based on updated technology and methodology used in the submission process.

 

Kathleen

 

 

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Oliver Pelz | 17 Oct 09:34 2014

GBRowse CGI-Parameter "add" is not working on my installation

Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver

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Nadine Elpida Tatto | 16 Oct 11:21 2014
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2 Problems concerning track loading/Error Message

Hi there,

I've come to administrate a gbrowse2 which I didn't set up by myself and ran into some problems
now.http://www.pichiagenome.org/ is the site

1) Most of the time there is an error message popping up I can't figure out the reason for:
------------- EXCEPTION: Bio::Root::Exception ------------- MSG: getting the feature_ids failed
STACK: Error::throw STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:472 STACK:
Bio::DB::Das::Chado::_by_alias_by_name
/usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1527 STACK:
Bio::DB::Das::Chado::get_feature_by_name
/usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1340 STACK:
Bio::Graphics::Browser2::Region::_feature_get
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:344 STACK:
Bio::Graphics::Browser2::Region::lookup_features
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:266 STACK:
Bio::Graphics::Browser2::Region::search_db
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:205 STACK: Bio::Graphics::Browser2::Region::search_feature
 s /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Region.pm:151 STACK:
Bio::Graphics::Browser2::RegionSearch::search_features_locally
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:412 STACK:
Bio::Graphics::Browser2::RegionSearch::search_features
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/RegionSearch.pm:301 STACK:
Bio::Graphics::Browser2::Render::region
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1137 STACK:
Bio::Graphics::Browser2::Render::segment
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1191 STACK:
Bio::Graphics::Browser2::Render::_update_state
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1898 STACK:
Bio::Graphics::Browser2::Render::update_state
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:1888 STACK
 : Bio::Graphics::Browser2::Render::run
/usr/local/lib/perl/5.10.1/Bio/Graphics/Browser2/Render.pm:290 STACK:
/usr/lib/cgi-bin/gb2/gbrowse:50 

2) The tracks were loading without problems 2 or 3 weeks ago, but now without any reason they don't load anymore

This stuff occures with IE, Chrome and Firefox, so I assume it does not depend on the browser.

I would appreciate any hint for solving this problems

Thank you

Nadine

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Oliver Pelz | 15 Oct 17:11 2014

cannot set admin password

Hi!

I am just installed GBrowse and run into trouble:

* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55

right after installation first thing I did without touching anything (not GBrowse.conf etc. ):

sudo -uapache ./gbrowse_set_admin_passwd.pl

gives me:

Use of uninitialized value in warn at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Session.pm line 153, <STDIN> line 2.
[20194] session lock timed out on request after 50.000s
: http://localhost  at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Session.pm line 153, <STDIN> line 2.
No SMTP server found in globals at /usr/local/lib64/perl5/Bio/Graphics/Browser2/SendMail.pm line 29, <STDIN> line 2.
No SMTP server found in globals at /usr/local/lib64/perl5/Bio/Graphics/Browser2/SendMail.pm line 29, <STDIN> line 2.
Mail Error

Am I missing something?
If I manually increase the lock time in Session.pm I get the same result.

Best,
Oliver Pelz
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Allen Qiu | 13 Oct 10:46 2014

Is Perlbrew instead of the default/system-wide Perl OK for Gbrowser?

Hi all,
Is it OK to use perlbrew to install another copy of perl&modules under my home directory, since I don't have root to install required perl modules? If so, how should I let the linux(RHEL)/Gbrowser/Apache? to use my local perl instead of the system's?
Regards,
Allen
 
 
2014-10-13
Allen Qiu
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Sofia Robb | 7 Oct 22:28 2014

double glyphs

Hi,

I am having a weird problem that I swear I wasn't having last time I looked.  I have all my gene tracks duplicated. When I check the db, they are only there once. What is going on?


drupal=> select * from feature where name like '%SMED30001441%';
 feature_id | dbxref_id | organism_id |       name        |                      uniquename                       | residues | seqlen | md5checksum | type_id | is_analysis | is_obsolete |      timeaccessioned       |      timelastmodified
------------+-----------+-------------+-------------------+-------------------------------------------------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
     159992 |           |          13 | SMED30001441-gene | maker-v31.001332-exonerate_est2genome-gene-0.2        |          |        |             |     818 | t           | f           | 2014-09-13 15:19:13.184188 | 2014-09-13 15:19:13.184188
     159993 |           |          13 | SMED30001441      | maker-v31.001332-exonerate_est2genome-gene-0.2-mRNA-1 |          |        |             |     349 | t           | f           | 2014-09-13 15:19:13.184188 | 2014-09-13 15:19:13.184188

Thanks,
Sofia
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Lau, Branden M - (bmlau | 2 Oct 21:55 2014
Picon

Displaying variants on GBrowse and/or JBrowse

Hello,

I'm trying to figure out how to use genome browsers to display either vcf data or gff3 data. I've tried uploading a gff file containing arabidopsis data onto TAIR's genome browser (http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/)http://tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/ and no matter where I look on the genome, I see no variants displayed. I want to know if someone can explain to me how to display variants onto GBrowse (or JBrowse for that matter) and whether or not I'm missing something obvious that someone can explain to me? 

I've attached the files I've been trying to use, one is a vcf file and the other is a gff3 formatted version of the vcf file. 

Thanks,
Branden
Attachment (iplant_vcf_to_gff.gff): application/octet-stream, 32 KiB
Attachment (Outputfile): application/octet-stream, 17 KiB
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Gmane