Mercurial > repos > jesse-erdmann > tapdance
diff lib/tapdance_base_config.pl @ 0:1437a2df99c0
Uploaded
author | jesse-erdmann |
---|---|
date | Fri, 09 Dec 2011 11:56:56 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/tapdance_base_config.pl Fri Dec 09 11:56:56 2011 -0500 @@ -0,0 +1,88 @@ +use DBI; + +##### +# Database configuration +##### +# +# Specify the username to connect to the database as +#$db_username="MY_DB_USERNAME"; +# +# Specify the password for the DB user +#$db_password="MY_DB_PASSWORD"; +# +# The software running the application +# Currently supported: +# * MySQL (Several database operations use MySQL specific SQL) +#$db_type='mysql'; +# +# The machine name or IP address to connect to the database on +#$db_host="127.0.0.1"; +# +# The port that the database is listening to on the host +#$db_port='3306'; +# +# The database to use for TAPDANCE +#$db_name="MY_TAPDANCE_DB"; +#$db_name="MY_DB"; +# +# Collapse db config to a single connection string +#$data_source = "dbi:$db_type:dbname=$db_name:$db_host;mysql_local_infile=1:$db_port"; +# +# Connect to the daatbase, running 'perl ./tabdance_base_config.pl +# can be used to verfiy the database configuration +#$dbh = DBI->connect($data_source, $db_username, $db_password, { RaiseError => 1, AutoCommit => 0 }); +# +# The name of the table to collect top level project information +$project_table_name = "TAPDANCE_project_master"; + +##### +# Required project dependant config variables +##### +# Project Name +#$proj = 'ProjName'; + +# Environment Directory or the top level directory for the project +# Contents will be as follows +# * CIS (directory containing intermediary files generated during CIS calculation) +# * config.pl (this file) +# * data (data inputs) +# * barcode2lib.txt (barcode to library name mapping, phase 1) +# * seq.tab (tabular sequence data, phase 1) +# * FISH (directory containing intermediary files generated during Fisher exact tests) +# * lib (executable code and some resources used by code) +# * mapping (directory containing intermediary files generated during mapping to the reference genome) +# * results (directory containing final outputs) +#$envDir = 'DirectoryName'; + +##### +# Config variables for insertion analysis +##### +# Specify the alignment + +# Specify the bowtie command to use, useful if you want to use a specific bowtie version not on the path +# or would like special options. For example, to quiet bowtie output. Defaults to 'bowtie' on user $PATH +$bowtie_exe='bowtie --quiet'; + +# Specify the genome idnex to use, should be a full path excluding the file extension or just the name of +# the genome index if the index is in the indexes folder of the bowtie installation. Defaults to 'mm9' +#$bowtie_idx = '/project/ccbioinf/Software/bowtie_indexes/mus_musculus_ncbi37'; +$bowtie_idx='mm9'; + +# Specify the IRDR string to use, see common options below, defaults to a Sleeping Beauty mutagen +# '__GTATGTAAACTTCCGACTTCAACTG' +$mutagens="__GTATGTAAACTTCCGACTTCAACTG"; + +##### +# Config variables for CIS calling +##### +# The interval file of features to annotate CIS calls with +$annotation_file="lib/mm9.bed"; +# +$library_percent ='0.0001'; +# +$CIS_total_pvalue = '0.05'; +$CIS_library_pvalue = '0.05'; +$CIS_region_pvalue = '0.05'; +# +$cocis_threshold ='0.001'; +