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setting up pasa mysql
this Linux documentation is a work in progress... It's fairly straightforward, and I'm currently providing the very basic steps involved.
If you're using 'ubuntu' linux, an 'apt-get install mysql' will probably do the trick.
For the perl module DBD::mysql, running 'cpanm install DBD::mysql' and perhaps 'cpanm install DBI' is needed.
basic info on installing perl modules can be found here.
See the mysql configuration notes at bottom of page for remaining steps.
Try using homebrew for installations. It's a life-saver IMHO for Mac software installations. Note these are instructions based on my latest experience doing this on MacOSX Mojave.
Install mysql
brew install mysql
Install the mysql connector and openssl
brew install openssl mysql-connector-c
Install the perl DBD::mysql module
wget https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN/DBD-mysql-4.050.tar.gz
tar xvf DBD-mysql-4.050.tar.gz
cd cd DBD-mysql-4.050
perl Makefile.PL --mysql_config=/usr/local/mysql/bin/mysql_config
make
make install
Because there's now an issue with not being able to define environmental variables like LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH) and have it used on mac due to the new Mac System Integrity Protection, you'll need to sym-link the shared libraries directly to your /usr/local/lib/ area so they can be found by DBD::mysql
cd /usr/local/lib
ln -s /usr/local/mysql/lib/*dylib .
Now check that it works:
perl -MDBD::mysql -e 'print "Hello there!";'
If the above doesn't error out, there's a good chance that it was set up correctly.
What I like to do here is to create proxy 'pasa' reader and writer accounts that everyone can leverage for working with PASA.
Start mysql as root:
mysql -uroot
If you need a root password, include the '-p' parameter. Sometimes, default mysql installations come w/o root passwords set (so be sure to set one soon, if you haven't, for your own protection). sometimes you need to run it as root like so: 'sudo mysql -uroot -p'
Creating users:
# create a 'pasa_write' user destined for reading/writing/creating capabilities
create user 'pasa_write'@'localhost' identified by 'pasa_write_pwd';
# this below will allow user 'pasa_write' to create databases named with a _pasa suffix
# (and so not just any database name)
grant all privileges on `%_pasa`.* to 'pasa_write'@'localhost';
# create a 'pasa_access' user that we'll use for read-only database access.
# this is useful for generating reports, pasa-web access, etc., where read-only is best.
create user 'pasa_access'@'localhost' identified by 'pasa_access';
Note, these users and passwords should match what is specified in the 'PASA_HOME/pasa_conf/conf.txt' configuration file.
- PASA Pipeline Wiki Home
- Software Installation Instructions
- Running the Alignment Assembly Pipeline
- Leveraging RNA-Seq by the PASA Pipeline
- Build a comprehensive transcriptome database, integrating genome-guided and genome-free transcript reconstructions
- Genome annotation - comparisons and updates
- Alternative Splicing Analysis
- Other useful PASA applications
- Navigating PASA reports via Pasa Web
- Miscellaneous tidbits