Package: BIRCH
BIRCH - Biological Research Computing Hierarchy
Documentation
Data
Platforms
:
solaris-sparc, linux-intel, solaris-amd64, linux-x86_64, osx-x86_64
Installation
:
BIRCH
Programs
:
adaptercheck.py - Find potential read-through adapter contamination in sequencing reads
birch - biolegato interface for launching BIRCH programs
birchadmin - BIRCH administration tool
birchdb - BIRCH documentation database
birchenv.py - API methods for setting environment variables and platform detection
birchhome.py - modify paths in BIRCH parameter files for local BIRCH system
birchlib.py - Library functions for BIRCH utilities
birchprops - Set and modify properties of the local BIRCH installation, found in $BIRCH/local/admin/BIRCH.properties
birchscript.py - Library methods for BIRCH install-scripts
BIRCHSettings.py - Change settings for BIRCH
birchstats - Report statistics on BIRCH usage
BIRCHUserSettings.py - Set User's environment variables for BIRCH
browser.csh - Launch a default browser from another application
btail.py - Print the contents of a file beginning at line x
csv2phyl.sh - >>> csv2phyl.sh is obsolete. Instead, use phylcnv.py which handles a larger number of file formats
customdoc.py - String substitution for HTML files
dat2ace.py - Create ACeDB file objects for all data files in a directory
delgi.py - remove GI numbers from GenBank flatfiles, in compliance with the NCBI phase out of GI numbers
doc2ace.py - Create ACeDB file objects for all documenataion files in a directory
fastalen.py - separate fasta sequences by length
fil.py - create .fil files for use by FASTA
fixfq.py - Divide a fastq file into two files, one with validated reads, and the other with reads that do not comply with the fastq format
htmldoc.py - Create BIRCH HTML documentation from BIRCH and local databases
l-gbirchdb - >>>>It is used for editing the copy of lbirchdb in local-generic. When a NEW BIRCH install is done, this empty database becomes the lbirchdb database.
lbirchdb - Database for local documentation
makelinks.sh - Create symbolic links in the current directory, pointing to files in a source directory
makemenus.py - (deprecated) Create .GDEmenus files for all platforms
phylip.py - Classes used by Python scripts that run Phylip programs
pyc.py - compile a Python script into bytecode and creates pydoc HTML documentation
rmlauncher.py - removes platform-specific BIRCH launcher from user's desktop
ruler - Print a text ruler for use in numbering columns
taxfetch.py - Given a set of ACCESSION numbers create a file containing the corresponding NCBI taxonomy entries
UNINSTALL-birch.py - Uninstall a BIRCH system
uniqid.py - Encodes long names of sequences in a fasta file into short, unique numerical strings. Decodes file generated from encoded files, and restores original sequence names