I'm a student of bioinformatics and I am using the OrthoMCL tool using this command
./orthomclLoadBlast my_orthomcl/orthomcl.config my_orthomcl/similarSequence.txt
but I am getting the error
Can't connect to data source ' :mysqllocalinfile=1' because I can't
work out what driver to use (it doesn't seem to contain a
'dbi:driver:' prefix and the DBI_DRIVER env var is not set) at
/home/linux/Desktop/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm
line 56
DBI is already installed in my system, so why is it giving this error? How do I solve it?
You need database drivers to be installed for the DBI module to work with your database. In this case it looks like you need to install DBD::mysql.
It is possible that OrthoMCL omits the driver name and uses just dbi::, in which case you must set the environment variable DBI_DRIVER to mysql.
The proper answer must be in the documentation for OrthoMCL. Have you read it?
Update
Looking at the source for orthomclLoadBlast it looks like your config file is faulty. There is a chance that someone here is familiar with the utility, but you must publish orthomcl.config to stand a chance of getting any useful advice.
you should use mysql for the driver:
sample:
use DBI;
$dbh = DBI->connect('dbi:mysql:DBNAME','root','password')
Related
After a clean install of Windows 10 when I started to use MySQL workbench I have this error when I try to dump a database.
I could not find anything about it anywhere, the only thing I find are problems with phyton, but nothing related with Workbench.
Output after dumping a database:
08:29:00 Dumping foo(all tables)
Error executing task write() argument must be str, not bytes
08:29:01 Export of b'C:\\Users\\erick\\Documents\\dumps\\Dump20210121 (2).sql' has finished
And the output file is in blank, some ideas?
You can disable (uncheck) the option create schema. It is annoying but it works.
If you have the latest MySQL Workbench (8.0.23), just uninstall and install MySQL Workbench 8.0.20. That worked for me.
Another workaround to this issue is to edit wb_admin_export.py.
In dump_to_folder (line 1679) replace
self.out_pipe = open(path,"w")
with
self.out_pipe = open(path,"wb")
In dump_to_file (line 1957) replace
self.out_pipe = open(self.path,"w")
with
self.out_pipe = open(self.path,"wb")
If you a using version 8.0.23, update to 8.0.25 or above.... it will fix this issue
I am using oracle goldengate for mysql version 19.1. While login to mysql DB from ggsci I am getting below warning. I have checked file libssl-2.17.0-stub.so, this file is not
present in LD_LIBRARY_PATH also not present in my linux machine. Due to this warning login not happening hence extract is not starting. Also did set up environment variables like-
MYSQL_UNIX_PORT
MYSQL_HOME
OGG_MYSQL_OPT_SSL_CA
OGG_MYSQL_OPT_SSL_CERT
OGG_MYSQL_OPT_SSL_KEY
GGSCI > dblogin SOURCEDB DB#host:3306, USERID XXX PASSWORD XXXX
Getting below error-
!!! WARNING !!! --> libssl-2.17.0-stub.so
This is a stub library which can be used for linking only. It must not
be used as a runtime library. Please make sure this library is not found
in LD_LIBRARY_PATH.
Can someone please help me with this.
Can you follow the steps from this doc link, and install OpenSSL and set the PATH as needed:
Check out this topic:
6.4 Other Programs and Settings for MySQL
Doc link: https://docs.oracle.com/en/middleware/goldengate/core/19.1/installing/installing-mysql1.html#GUID-14BA87AB-194B-483C-AECF-151A31F4AFC1
Let us know if that resolves it.
I've been forced to try to port to PySide2 from PySide because I'm developing code (on Windows 7) used inside Maya and Maya 2017 has moved to PySide2.
PySide2 ships with Maya but only comes with the driver to talk to sqlite DBs. So I need to tell Qt about a new DIR that contains the MySql driver, like this:
from PySide2 import QtWidgets
QtWidgets.QApplication.addLibraryPath("C:\temp\plugins")
This DIR contains a sub sqldrivers DIR which contains the driver. This works- when I call QtSql.QSqlDatabase.drivers() the new one is there so I've got the right driver and it's being picked up.
However when I create a new DB and call open:
db = QtSql.QSqlDatabase.addDatabase("QMYSQL3")
db.setDatabaseName("my_db")
db.setHostName("host")
db.setUserName("user")
db.setPassword("password")
db.open()
the open command returns False and the DB is not accessible. I call:
db.lastError()
and get:
# Result: <PySide2.QtSql.QSqlError("", "Driver not loaded", "Driver not loaded") at 0x0000000075410C08> #
NB: we successfully did the exact same thing with the previous PySide version.
Other threads mention similar things and it turned out to be missing the actual libmysql.dll, which is the actual MySql DLL and can result in the same error if missing. However I definitely have this on my system and it's definitely in the PATH. It's actually the same file that is being successfully picked up through PySide. But the PySide2 driver just wont open a connection to the DB.
I suspect maybe a dodgy driver but wondered if anyone has any experience with this or any advice?
I had the same error, but with postgres.
I solved by placing the libpq.dll connector library next to my script.py.
Then for mysql it would be libmysql.dll.
In my case I had to build the libpq.dll from the source of postgres 9.6
It seems that with PySide2 it is not necessary to use:
QtWidgets.QApplication.addLibraryPath ("C: \ path_to\ plugins")
using:
print (PySide2.QtCore.QLibraryInfo.location (PySide2.QtCore.QLibraryInfo.PluginsPath)), I could see that the path was correct.
a greeting
I can't get the propel script running on my system.
My build.properties looks like this:
propel.project = test
# The Propel driver to use for generating SQL, etc.
propel.database = pgsql
# This must be a PDO DSN
propel.database.url = pgsql:host=localhost;port=5432;dbname=test
propel.database.user = user
propel.database.password = password
I get the following error when I run propel-gen . reverse:
[propel-schema-reverse] There was an error building XML from metadata:
/home/user/web/dev/vendor/propel/generator/build-propel.xml:296:1:
could not find driver
pdo_pgsql is enabled (there are several applications running it succesfully); but in my phpinfo there seems to be a wrong version stated:
PostgreSQL(libpq) Version 8.4.13
I'm running PostgreSQL 9.1. I think this causes the error but I have no idea why the versions are different. I have installed first PostGreSQL and then php5-fpm etc. via apt-get.
Using Php 5.3.5 on Ubuntu 11.04. Can somebody help?
Remove all empty spaces and newlines in between the xml tags in the buildtime-conf.xml. That worked for me.
My file looked like this after using the runtime-conf.xml as a template for the buildtime-conf.xml
...
<adapter>
mysql
</adapter>
...
Now it looks like that and it works
...
<adapter>mysql</adapter>
...
I'm having troubles with MySQL queries in Ruby. I use 'mysql' gem.
Configuration is stored in a separate yml file and loaded into #conf variable.
This is my code:
# connect to the database
Mysql::new(#conf['sql_host'], #conf['sql_user'], #conf['sql_password'], #conf['sql_base'])
# it's ok when we're doing this
my.query("SELECT * FROM `my_table`") do |e|
# code
end
# Maybe, I've missed something here...
# really this query will insert value into other table, used SELECT just for testing
# this throws exception: 'query: not connected'
my.query("SELECT * FROM `my_table_2`")
Windows XP
ruby 1.8.6 (2008-08-11 patchlevel 287) [i386-mswin32]
mysql (2.8.1, 2.7.3)
MySQL client version: 5.0.51a
Second query throws 'query: not connected'.
First of all, your program looks ok. I am 100% sure you have libmysql.dll version problem.
I can reproduce this with libmysql.dll provided from Mysql installer.
Download this file and replace in c:\ruby\bin\
http://instantrails.rubyforge.org/svn/trunk/InstantRails-win/InstantRails/mysql/bin/libmySQL.dll
and re-run your program without any change.
Related issue and credit to here
I have run into immeasurable problems when attempting to use Ruby's mysql gem on any version of Windows. From what I can tell, it simply doesn't work unless you can figure out how to compile it yourself (which is a royal pain in the ass).
Have you considered using ActiveRecord as your ORM (object relational mapping) layer and doing development with SQLite or some other database on Windows and then running the production environment on Linux with MySQL? This is the solution that I took a while back and it worked out quite well.