Question: USCS hgsql Operation not permitted ERROR
0
gravatar for 2013302630028
2.8 years ago by
201330263002810 wrote:

When I use the kent scource to install USCS mirror, I get an error in testing hgsql: sqreb@sqreb-Vostro-1450:~$ hgsql -e "show tables;" hgcentral Error reading 4096 bytes: Operation not permitted The details of installation process is in below. Thank you.

I set environment as:

sqreb@sqreb-Vostro-1450:~$ mysql_config --include
-I/usr/local/mysql/include
sqreb@sqreb-Vostro-1450:~$ mysql_config --libs
-L/usr/local/mysql/lib -lmysqlclient -lpthread -lm -lrt -ldl
export MACHTYPE=x86_64
export MYSQLINC="/usr/include/mysql"
export MYSQLLIBS="-L/usr/local/mysql/lib -lmysqlclient -lpthread -lm -lrt -ldl"

And make those src file:

     src/lib
     src/jkOwnLib
     scr/hg/lib
     scr/htslib
     scr/utils
     scr/hg/utils
     scr/hg/bedSort
     src/gfServer
     src/gfClient
     src/blat
     src/utils/faToNib

Set MySQL conference file as:

/etc/my.cnf

[mysqld]
# UCSC
local-infile=1
default-storage-engine=MYISAM

sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES 

#UCSC
[client]
local-infile=1

$WEBROOT/cgi-bin/hg.conf

###########################################################
# Config file for the UCSC Human Genome server
#
# the format is in the form of name/value pairs
# written 'name=value' (note that there is no space between
# the name and its value.
#
#   This file last updated:
#   $Id: ex.hg.conf,v 1.27 2010/06/10 05:16:06 markd Exp $
#
###########################################################
# db.host is the name of the MySQL host to connect to
#  high-volume sites will want a separate database server from the web server
db.host=localhost
# db.user is the username is use when connecting to the specified db.host
#   it needs read-only access.  The browser CGIs do not need
#   read-write access to the database tables
db.user=readonly
# db.password is the password to use with the specified db.user
db.password=access

# if you want a different default species selection on the Gateway
# page, change this default Human to one of the genomes from the
#   defaultDb table in hgcentral:
#   hgsql -e "select genome from defaultDb;" hgcentral
# If you need a different version of that specific genome, change
#   the defaultDb table entry, for example, a different mouse genome
#   version as default:
#   hgsql -e 'update defaultDb set name="mm8" where genome="Mouse"
#   then this defaultGenome would read: defaultGenome=Mouse
# 
defaultGenome=Human

# track group table definitions.  This is a comma-seperate list similar to
# db.trackDb that defines the track group tables.  Database profiles 
# may alow be included using the syntax dbProfile:grpTbl.
db.grp=grp
#db.grp=grp_local,grp
#db.grp=grp,someDbProfile:grp

# New browser function as of March 2007.  Future browser code will
#   have this on by default, and can be turned off with =off
#   Initial release of this function requires it to be turned on here.
browser.indelOptions=on

# Do not show the generic 500 Apache error, but show the browser error message
# instead to the user. 
showEarlyErrors=on
# The opposite: try to suppress very early errors as far as possible as
# show a 500 Apache error instead. This somewhat reduces the options for
# Cross-Site-Scripting attacks but makes it harder for users to find out
# what caused an error, e.g. in custom tracks.
# suppressVeryEarlyErrors=on

# central.host is the name of the host of the central MySQL
# database where stuff common to all versions of the genome
# and the user database is stored.
central.db=hgcentral
central.host=localhost
#
# Be sure this user has UPDATE AND INSERT privs for hgcentral
#   The central.domain will allow the browser cookie-cart
#   function to work.  Set it to the domain of your Apache
#   WEB server.  For example, if your browser URL is:
#   http://mylab.university.edu/cgi-bin/hgTracks?db=hg19
#   set central.domain to: mylab.university.edu
#   An exception to this is when multiple virtual hosts share the
#   same central database and central.cookie setting (see below).
#   In #that case, domain should be inclusive of all virtual hosts
#   (e.g. only #.university.edu).
#       The special value HTTPHOST will set the domain to whatever
#       servername was sent with the last HTTP request. This allows cookies
#       to work if a server has multiple names.
central.user=readwrite
central.password=update
central.domain=mylab.university.edu
# use this cookie setting to keep your installation hguid cookie setting
#   distinct from UCSC hguid cookie.  If you have *multiple* central
#   databases for multiple hosts, set a distinct cookie name per
#   central database.
# central.cookie=hguid.mylab
#   personalize the background of the browser with a specified jpg
#   floret.jpg is the standard UCSC default
browser.background=../images/floret.jpg

# optional location of grepIndex files
grepIndex.genbank=/data/tmp/grepIndex
grepIndex.default=/gbdb

#  new option for track reording functions, August 2006
hgTracks.trackReordering=on
#   in case of failure of the above central.host machine,
#   the following settings will be used to access a secondary
#   mirror of the database
backupcentral.db=hgcentral
backupcentral.host=localhost
backupcentral.user=readwrite
backupcentral.password=update
#   archivecentral settings are used for archived assemblies
#   that have been moved to a different machine.
archivecentral.db=hgcentral
archivecentral.host=localhost
archivecentral.user=readwrite
archivecentral.password=update

# Parallel fetching of remote network resources using bigDataUrl such
#       as trackHubs and customTracks
# how many threads to use (set to 0 to disable)
parallelFetch.threads=20
# how long to wait in seconds for parallel fetch to finish
parallelFetch.timeout=90

# These settings enable geographic allele frequency images on the 
# details pages for the HGDP Allele Frequency (hgdpGeo) track.
# (HGDP = Human Genome Diversity Project)
# Programs required for per-SNP geographic maps of HGDP population
# allele frequencies:
hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy
hgc.ps2rasterPath=/hive/data/outside/GMT4.3.1/bin/ps2raster
hgc.ghostscriptPath=/usr/bin/ghostscript

~/.hg.conf

[mysqld]
db.user=browser
db.password=genome
central.user=browser
central.password=genome
central.db=hgcentral

And the MySQL detail is below:

mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| hgTemp             |
| hgcentral          |
| mysql              |
| performance_schema |
| sacCer3            |
| sys                |
+--------------------+

mysql> select User,Host from user;
+-----------+-----------+
| User      | Host      |
+-----------+-----------+
| browser   | localhost |
| mysql.sys | localhost |
| readonly  | localhost |
| readwrite | localhost |
| root      | localhost |
| sqreb     | localhost |
+-----------+-----------+
6 rows in set (0.00 sec)

sqreb@sqreb-Vostro-1450:~$ mysql -ubrowser -pgenome -e "show databases;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+--------------------+
| Database           |
+--------------------+
| information_schema |
| hgTemp             |
| hgcentral          |
| mysql              |
| performance_schema |
| sacCer3            |
| sys                |
+--------------------+


sqreb@sqreb-Vostro-1450:~$ mysql -ureadonly -paccess -e "show databases;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+--------------------+
| Database           |
+--------------------+
| information_schema |
| hgTemp             |
| hgcentral          |
| mysql              |
| performance_schema |
| sacCer3            |
| sys                |
+--------------------+

sqreb@sqreb-Vostro-1450:~$ mysql -ureadwrite -pupdate -e "show databases;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+--------------------+
| Database           |
+--------------------+
| information_schema |
| hgTemp             |
| hgcentral          |
| mysql              |
| performance_schema |
| sacCer3            |
| sys                |
+--------------------+
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 2.8 years ago by 201330263002810

Can you please try hgsql -e "show databases" and hgsql --help . The second one should give all the options it is configured with.

ADD REPLYlink written 2.8 years ago by microfuge1.1k
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