[ensembl-dev] Fwd: Ensembl Website not working

manoj nainwal manoj92nainwal at gmail.com
Wed Oct 12 06:26:30 BST 2016


Hi,

I am trying to set up Ensembl website on my system. I followed the given
steps on you website to set up Ensembl locally. But there are some problems
I am facing while try to run ensembl server.

My directory structure is :

--- /usr/local/ensembl
               ---- apache2
               ---- ensembl
               ---- bioperl-live
               ---- ensembl-compara
               ---- ensembl-funcgen
               ---- ensembl-git-tools
               ---- enesmbl-io
               ---- ensembl-orm
               ---- ensembl-tools
               ---- ensembl-variation
               ---- ensembl-webcode
               ---- lib
               ---- logs
               ---- public-plugins
               ---- tabix

If I try "/usr/local/ensembl/apache2/bin/httpd -d /usr/local/ensembl" to
run server then  I got error -
that conf folder is not present in /usr/local/ensembl.
But conf present in /usr/local/ensembl/ensembl-webcode/conf, so I created a
soft link to this conf.
and again tried to run the same command and also set the modules soft link
too.
then I got error-
------------------------------------------------------------
------------------------------------------------------------
------------------
 Starting up as non-mirror machine
 Server has identities

############################################################
##################
# Species "Homo_sapiens" not defined in ENSEMBL_SPECIES_ALIASES
############################################################
##################
############################################################
##################
# Species "" not defined in ENSEMBL_SPECIES_ALIASES
############################################################
##################
 Starting up Ensembl server on host: scsor0006085001.rtp.
openenglab.netapp.com

Syntax error on line 152 of /usr/local/ensembl/conf/httpd.conf:
Unknown type 'CODE' for directive PidFile at
/usr/local/lib/perl/5.18.2/Apache2/PerlSections.pm
line 198.\n
------------------------------------------------------------
------------------------------------------------------------
-------------------

And if I try to run "/usr/local/ensembl/ensembl-
webcode/ctrl-scripts/restart_server -r" then again it shows some error -
------------------------------------------------------------
-------------------------------------------------------------------------
Syntax error on line 152 of /usr/local/ensembl/ensembl-web
code/conf/httpd.conf:
panic: sv_setpvn called with negative strlen -1 at
/usr/local/ensembl/ensembl/modules/Bio/EnsEMBL/Utils/Exception.pm line
421.\n
 Could not start server: No such file or directory.
[FATAL] Server start failed.
---------------------------------------------------------------------

And one thing it shows that **host.httpd.pid" file is not there in logs
folder.

And what is the correct command to run ensembl-server ?
1. /usr/local/ensembl/apache2/bin/httpd -d /usr/local/ensembl ( do I have
to make softlink ?)
2.  /usr/local/ensembl/apache2/bin/httpd -d /usr/local/ensembl/ensembl-
webcode
3. /usr/local/ensembl/ensembl-webcode/ctrl-scripts/restart_server -r

Kindly help me to solve it.

Thanks
Manoj
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