Mercurial > repos > iuc > kobas
changeset 1:b573ecb2ca66 draft
planemo upload commit 7a37f337506adeecf03370e471903abbbd49db5c-dirty
| author | iuc |
|---|---|
| date | Sat, 05 Nov 2016 10:31:30 -0400 |
| parents | 720b1beabad6 |
| children | 2f9619adab91 |
| files | tool-data/blastdb_d.loc.sample |
| diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb_d.loc.sample Sat Nov 05 10:31:30 2016 -0400 @@ -0,0 +1,57 @@ +# 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.