Hello,
I’m trying to set up the SequenceServer 1.10- alpha on my Ubuntu 16.04 workstation with Apache 2.4.18 and last version of Passenger for sharing Blast databases with our community. We’ve been using successfully older version of the software with multiple database directories setup.
My current installation does not give me any errors - access.log, error.log as well as /tmp directory log files are all good, command line sequenceserver gives the list of databases etc, but all I can see on the page is the header and footer with the logos and an empty tiny frame for the list of databases.
Clicking on the Sequenceserver logo sends me right to the Help page.
My config.ru file is modified to point to a different than default configuration file that contains path to the database directory as suggested in the documentation. My attempt to point to a different DOTDIR in the config.ru resulted in an error.
Any suggestions from this group will be greatly appreciated.
Pull and try again. Best way to try stuff alpha stuff is with -D flag (same as setting ENV[‘RACK_ENV’] = ‘development’ in config.ru just before SequenceServer.init).
Also, it’s 1.1.0-alpha.
Priyam
Hello Priyam,
I did pull and tried to run the application as suggested, in the development environment. Problem remains the same. Here is the snippet from the apache error.log file:
[Wed Jan 11 07:35:02.023613 2017] [mpm_event:notice] [pid 1999:tid 1404914842970
88] AH00489: Apache/2.4.18 (Ubuntu) Phusion_Passenger/5.1.1 configured – resumi
ng normal operations
[Wed Jan 11 07:35:02.023633 2017] [core:notice] [pid 1999:tid 140491484297088] A
H00094: Command line: ‘/usr/sbin/apache2’
[ 2017-01-11 07:35:05.2392 10966/7f7b19e02700 age/Cor/SecurityUpdateChecker.h:35
0 ]: Security update check: no update found (next check in 24 hours)
App 13158 stdout:
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Reading configuration file: /home
/seqserv/.sequenceserver.conf.
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Location of NCBI BLAST+ not provi
ded. Assuming NCBI BLAST+ to be present in: $PATH
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Will use BLAST+ databases at: /ho
me/seqserv/blast_databases/CLS_CY
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Executing: blastdbcmd -recursive
-list /home/seqserv/blast_databases/CLS_CY -list_outfmt “%f %t %p
%n %l %d”
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Found nucleotide database ‘E. fes
tucae E1017 Sc B9.5’ at ‘/home/seqserv/blast_databases/CLS_CY/E1017_B_9_5_scaffo
lds.fasta’
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Found nucleotide database ‘E. fes
tucae E7626 Sc B9.5’ at ‘/home/seqserv/blast_databases/CLS_CY/E7626_B_9_5_scaffo
lds.fasta’
App 13158 stderr: [2017-01-11 09:08:20] DEBUG Will use 1 threads to run BLAST.
App 13245 stdout:
App 13158 stderr: [2017-01-11 09:08:21] DEBUG {}
And the access.log:
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/css/seq
uenceserver.min.css HTTP/1.1” 200 36237 “http://sawa.ca.uky.edu/blast_CLS_genome
s/” “Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.
0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/sequenc
eserver.min.js HTTP/1.1” 200 254170 “http://sawa.ca.uky.edu/blast_CLS_genomes/”
“Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/fonts/S
ource_Sans_Pro_400.woff2 HTTP/1.1” 200 14570 “http://sawa.ca.uky.edu/blast_CLS_g
enomes/css/sequenceserver.min.css” “Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:5
0.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/vendor/
npm/font-awesome@4.4.0/fonts/fontawesome-webfont.woff2?v=4.4.0 HTTP/1.1” 200 647
26 “http://sawa.ca.uky.edu/blast_CLS_genomes/css/sequenceserver.min.css” “Mozill
a/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/shims/s
tyles/shim.css HTTP/1.1” 200 3255 “http://sawa.ca.uky.edu/blast_CLS_genomes/” “M
ozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/shims/f
orm-core.js HTTP/1.1” 200 2532 “http://sawa.ca.uky.edu/blast_CLS_genomes/” “Mozi
lla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /favicon.ico HTTP/1.1” 404
506 “-” “Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefo
x/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/shims/f
orm-validation.js HTTP/1.1” 200 6741 “http://sawa.ca.uky.edu/blast_CLS_genomes/”
“Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/shims/f
orm-combat.js HTTP/1.1” 200 1400 “http://sawa.ca.uky.edu/blast_CLS_genomes/” “Mo
zilla/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
128.163.193.150 - - [11/Jan/2017:09:08:21 -0500] “GET /blast_CLS_genomes/shims/d
om-extend.js HTTP/1.1” 200 6539 “http://sawa.ca.uky.edu/blast_CLS_genomes/” “Moz
illa/5.0 (X11; Ubuntu; Linux x86_64; rv:50.0) Gecko/20100101 Firefox/50.0”
I am about to give up and install dockerized version with the ngix reverse proxy. It’s probably a better, modern and safer solution.
I just hate to leave things unresolved like that.
Ah, the alpha version is currently not a smooth sail for sub-uri deployment. Plan is to fix it much closer to a release. But given your interest, I will try to take a look over the weekend.
Priyam