diff lib/tapdance_base_config.pl @ 0:1437a2df99c0

Uploaded
author jesse-erdmann
date Fri, 09 Dec 2011 11:56:56 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/tapdance_base_config.pl	Fri Dec 09 11:56:56 2011 -0500
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+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';
+