TWO Installation Questions | MySQL & "missing" dependencies on 18.02

[Andor Kiss]

I ***think*** I've followed all the instructions on getting PASA installed on Ubuntu 18.04 for use with Augustus such that I can train Augustus to generate a "training species" (Xenopus tropicalis) for use with BUSCO, which to my knowledge hasn't been done yet.  My goal is to use Xt in Augustus for evaluation with BUSCO to find genes to check completeness of the wood frog assembly, as the default of "human" doesn't make too much sense to me...

Anyway, I had two questions:

(1) In the MySQL configuration file for PASA (e.g. on my machine <cbfgws6>; </home/cbfgws6/Programs/PASApipeline/pasa_conf/conf.txt>), I read "# This file is not used if SQLITEDB is set in the alignment assembly configuration file".  Where do I set that variable/path?  Would that be in the <pasa.alignAssembly.Template.txt> file? And what would be the [# database settings
DATABASE=<__DATABASE__>] variable?  If so, what do I change it to?  My MySQL database is MYSQLSERVER=localhost.  Finally, where would I place this <pasa.alignAssembly.Template.txt> edited file? You say in the "individual working directories" - does this mean whereever one is launching PASA from?  I'm a little unclear how this would work in conjunction with the Augustus training script.

(2)  In the DOCKER instructions, there are some install commands for all the dependencies:

apt-get update && apt-get install -y gcc g++ perl python automake make \
wget git curl libdb-dev \
zlib1g-dev bzip2 libncurses5-dev \
texlive-latex-base \
default-jre \
python-pip python-dev \
gfortran \
build-essential libghc-zlib-dev libncurses-dev libbz2-dev liblzma-dev libpcre3-dev libxml2-dev \
libblas-dev gfortran git unzip ftp libzmq3-dev nano ftp fort77 libreadline-dev \
libcurl4-openssl-dev libx11-dev libxt-dev \
x11-common libcairo2-dev libpng12-dev libreadline6-dev libjpeg8-dev pkg-config libtbb-dev \ && apt-get clean

Some of these can't be installed on 18.04 (e.g. libpng12-dev) due to conflicts with remove r-base-dev.  If I've managed to compile all the other components (PASA, BLAT, FASTA, GMAP, MySQL-server; CPAN modules), am I "good" or has there been a failover that I likely missed.

Thanks,

Andor

[Brian Haas]

Hi Andor,

I'm not sure how this is integrated with Augustus, but I can comment on the pasa-specific issues below

On Thu, Aug 6, 2020 at 5:54 PM Andor Kiss <andor...@gmail.com> wrote:

I ***think*** I've followed all the instructions on getting PASA installed on Ubuntu 18.04 for use with Augustus such that I can train Augustus to generate a "training species" (Xenopus tropicalis) for use with BUSCO, which to my knowledge hasn't been done yet.  My goal is to use Xt in Augustus for evaluation with BUSCO to find genes to check completeness of the wood frog assembly, as the default of "human" doesn't make too much sense to me...

Anyway, I had two questions:

(1) In the MySQL configuration file for PASA (e.g. on my machine <cbfgws6>; </home/cbfgws6/Programs/PASApipeline/pasa_conf/conf.txt>), I read "# This file is not used if SQLITEDB is set in the alignment assembly configuration file".  Where do I set that variable/path?  Would that be in the <pasa.alignAssembly.Template.txt> file? And what would be the [# database settings
DATABASE=<__DATABASE__>] variable?  If so, what do I change it to?  My MySQL database is MYSQLSERVER=localhost.  Finally, where would I place this <pasa.alignAssembly.Template.txt> edited file? You say in the "individual working directories" - does this mean whereever one is launching PASA from?  I'm a little unclear how this would work in conjunction with the Augustus training script.

If you're using sqlite as the backend instead of mysql, then the settings here shouldn't matter.  If you're using mysql, then you set the mysql variables in that conf file to what's needed for accessing the mysql database server. These are general mysql config settings.  The file would exist as ${PASAHOME}/pasa_conf/conf.txt  so the pasa scripts will find it where needed.

The pasa alignmentAssembly config is specific to a given pasa execution. Every different target data set  (genome and transcript set) requires a separate pasa database to be created.  This alignmentAssembly.config includes information about the database to be used on whatever backend (sqlite or mysql). If you're using sqlite, then set the DATABASE=/full/path/to/where/you/want/your/sqlite/db/to/be/created.sqlite   and PASA will know that you're in sqlite-mode.   If you're using mysql, then you just specify the name of the mysql db that will be created and used on the mysql server.

 

(2)  In the DOCKER instructions, there are some install commands for all the dependencies:

apt-get update && apt-get install -y gcc g++ perl python automake make \
wget git curl libdb-dev \
zlib1g-dev bzip2 libncurses5-dev \
texlive-latex-base \
default-jre \
python-pip python-dev \
gfortran \
build-essential libghc-zlib-dev libncurses-dev libbz2-dev liblzma-dev libpcre3-dev libxml2-dev \
libblas-dev gfortran git unzip ftp libzmq3-dev nano ftp fort77 libreadline-dev \
libcurl4-openssl-dev libx11-dev libxt-dev \
x11-common libcairo2-dev libpng12-dev libreadline6-dev libjpeg8-dev pkg-config libtbb-dev \ && apt-get clean

Some of these can't be installed on 18.04 (e.g. libpng12-dev) due to conflicts with remove r-base-dev.  If I've managed to compile all the other components (PASA, BLAT, FASTA, GMAP, MySQL-server; CPAN modules), am I "good" or has there been a failover that I likely missed.

If some of the library names changed for ubuntu 18, you can probably just switch to using the newer library and I expect it'll be fine.   If you can use docker instead, then I'd suggest using the docker image we provide. 

hth,

~b

 

Thanks,

Andor

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas