view tool-data/blastdb_d.loc.sample @ 19:a212d2984601 draft

v0.2.00, fix tool_dependencies.xml version

# This is a sample file distributed with Galaxy that is used to define a
# list of protein domain databases, using three columns tab separated
# (longer whitespace are TAB characters):
#
# <unique_id>{tab}<database_caption>{tab}<base_name_path>
#
# The captions typically contain spaces and might end with the build date.
# It is important that the actual database name does not have a space in
# it, and that there are only two tabs on each line.
#
# You can download the NCBI provided databases as tar-balls from here:
# ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/
#
# For simplicity, many Galaxy servers are configured to offer just a live
# version of each NCBI BLAST database (updated with the NCBI provided
# Perl scripts or similar). In this case, we recommend using the case
# sensistive base-name of the NCBI BLAST databases as the unique id.
# Consistent naming is important for sharing workflows between Galaxy
# servers.
#
# For example, consider the NCBI Conserved Domains Database (CDD), where
# you have downloaded and decompressed the files under the directory
# /data/blastdb/domains/ meaning at the command line BLAST+ would be
# run as follows any would look at the files /data/blastdb/domains/Cdd.*:
#
# $ rpsblast -db /data/blastdb/domains/Cdd -query ...
#
# In this case use Cdd (title case to match the NCBI file naming) as the
# unique id in the first column of blastdb_d.loc, giving an entry like
# this:
#
# Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/domains/Cdd
#
# Your blastdb_d.loc file should include an entry per line for each "base name"
# you have stored. For example:
#
# Cdd{tab}NCBI CDD{tab}/data/blastdb/domains/Cdd
# Kog{tab}KOG (eukaryotes){tab}/data/blastdb/domains/Kog
# Cog{tab}COG (prokaryotes){tab}/data/blastdb/domains/Cog
# Pfam{tab}Pfam-A{tab}/data/blastdb/domains/Pfam
# Smart{tab}SMART{tab}/data/blastdb/domains/Smart
# Tigr{tab}TIGR	/data/blastdb/domains/Tigr
# Prk{tab}Protein Clusters database{tab}/data/blastdb/domains/Prk
# ...etc...
#
# Alternatively, rather than a "live" mirror of the NCBI databases which
# are updated automatically, for full reproducibility the Galaxy Team
# recommend saving date-stamped copies of the databases. In this case
# your blastdb_d.loc file should include an entry per line for each
# version you have stored. For example:
#
# Cdd_05Jun2010{tab}NCBI CDD 05 Jun 2010{tab}/data/blastdb/domains/05Jun2010/Cdd
# Cdd_15Aug2010{tab}NCBI CDD 15 Aug 2010{tab}/data/blastdb/domains/15Aug2010/Cdd
# ...etc...
#
# See also blastdb.loc which is for any nucleotide BLAST database, and
# blastdb_p.loc which is for any protein BLAST databases.