CLIPSeqTools::CompareApp::all - Run all clipseqtools-compare analyses.
clipseqtools-compare all [options/parameters]
Run all clipseqtools-compare analyses.
Takes two libraries (one called input and one called reference) on which all single clipseqtools analyses have ran. Assumes that all single clipseqtools analyses used a common o_prefix for each library.
Input options for library. --driver <Str> driver for database connection (eg. mysql, SQLite). --database <Str> database name or path to database file for file based databases (eg. SQLite). --table <Str> database table. --host <Str> hostname for database connection. --user <Str> username for database connection. --password <Str> password for database connection. --records_class <Str> type of records stored in database. --filter <Filter> filter library. May be used multiple times. Syntax: column_name="pattern" e.g. keep reads with deletions AND not repeat masked AND longer than 31 --filter deletion="def" --filter rmsk="undef" . --filter query_length=">31". Operators: >, >=, <, <=, =, !=, def, undef --res_prefix <Str> results prefix of clipseqtools analysis. Should match the o_prefix used when running clipseqtools on the library. Input options for reference library. --r_driver <Str> driver for database connection (eg. mysql, SQLite). --r_database <Str> database name or path to database file for file based databases (eg. SQLite). --r_table <Str> database table. --r_host <Str> hostname for database connection. --r_user <Str> username for database connection. --r_password <Str> password for database connection. --r_records_class <Str> type of records stored in database. --r_filter <Filter> same as filter but for reference library. --r_res_prefix <Str> results prefix of clipseqtools analysis. Should match the o_prefix used when running clipseqtools on the reference library. Other input. --rname_sizes <Str> file with sizes for reference alignment sequences (rnames). Must be tab delimited (chromosome\tsize) with one line per rname. Output --o_prefix <Str> output path prefix. Script will create and add extension to path. Default: ./ Other options. -v --verbose print progress lines and extra information. -h -? --usage --help print help message
To install CLIPSeqTools, copy and paste the appropriate command in to your terminal.
cpanm
cpanm CLIPSeqTools
CPAN shell
perl -MCPAN -e shell install CLIPSeqTools
For more information on module installation, please visit the detailed CPAN module installation guide.