comparison tool-data/blastdb_p.loc.sample @ 15:c16c30e9ad5b draft

Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)

14:2fe07f50a41e

#This is a sample file distributed with Galaxy that is used to define a
#list of protein BLAST databases, using three columns tab separated
#(longer whitespace are TAB characters):
#
#<unique_id>	<database_caption>	<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.
#
#So, for example, if your database is NR and the path to your base name
#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this:
#
#nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr
#
#and your /data/blastdb directory would contain all of the files associated
#with the database, /data/blastdb/nr.*.
#
#Your blastdb_p.loc file should include an entry per line for each "base name"
#you have stored. For example:
#
#nr_05Jun2010	NCBI NR (non redundant) 05 Jun 2010	/data/blastdb/05Jun2010/nr
#nr_15Aug2010	NCBI NR (non redundant) 15 Aug 2010	/data/blastdb/15Aug2010/nr
#...etc...
#
#You can download the NCBI provided protein databases like NR from here:
#ftp://ftp.ncbi.nlm.nih.gov/blast/db/
#
#See also blastdb.loc which is for any nucleotide BLAST database, and
#blastdb_d.loc which is for any protein domains databases (like CDD).

15:c16c30e9ad5b

# This is a sample file distributed with Galaxy that is used to define a
# list of protein BLAST databases, using three columns tab separated:
#
# <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 protein databases like NR from here:
# ftp://ftp.ncbi.nlm.nih.gov/blast/db/
#
# 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 "non-redundant" protein BLAST database
# where you have downloaded and decompressed the files under /data/blastdb/
# meaning at the command line BLAST+ would be run with something like
# which would look at the files /data/blastdb/nr.p*:
#
# $ blastp -db /data/blastdb/nr -query ...
#
# In this case use nr (lower case to match the NCBI file naming) as the
# unique id in the first column of blastdb_p.loc, giving an entry like
# this:
#
# nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr
#
# 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_p.loc file should include an entry per line for each
# version you have stored. For example:
#
# nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr
# nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr
# ...etc...
#
# See also blastdb.loc which is for any nucleotide BLAST database, and
# blastdb_d.loc which is for any protein domains databases (like CDD).