Mercurial > repos > iuc > kobas
changeset 2:2f9619adab91 draft
planemo upload commit 76744a97a6f837ee60104321867e6451fec78d74-dirty
| author | iuc |
|---|---|
| date | Sat, 05 Nov 2016 10:37:44 -0400 |
| parents | b573ecb2ca66 |
| children | 83b998fa34ea |
| files | tool-data/blastdb_d.loc.sample tool-data/blastdb_p.loc.sample |
| diffstat | 2 files changed, 44 insertions(+), 57 deletions(-) [+] |
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--- a/tool-data/blastdb_d.loc.sample Sat Nov 05 10:31:30 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -# 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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb_p.loc.sample Sat Nov 05 10:37:44 2016 -0400 @@ -0,0 +1,44 @@ +# 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).