Package: BIRCH

BIRCH - Biological Research Computing Hierarchy
Documentation
Data
Platforms: 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 csv2phyl.sh is obsolete.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 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 sql2htmldoc.py - create web documentation pages from birchdocdb databases 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