Mercurial > repos > devteam > ncbi_blast_plus
changeset 1:5e9d5e536b79 draft
Uploaded v0.1.02 preview 2, clarify sample blastdb loc files, etc
| author | peterjc |
|---|---|
| date | Tue, 03 Mar 2015 05:32:18 -0500 |
| parents | 432ea9614cc9 |
| children | 6119ddccd8a3 |
| files | tool-data/blastdb.loc.sample tool-data/blastdb_d.loc.sample tool-data/blastdb_p.loc.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/repository_dependencies.xml |
| diffstat | 5 files changed, 125 insertions(+), 81 deletions(-) [+] |
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--- a/tool-data/blastdb.loc.sample Fri Jan 30 08:27:28 2015 -0500 +++ b/tool-data/blastdb.loc.sample Tue Mar 03 05:32:18 2015 -0500 @@ -1,39 +1,44 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of nucleotide BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): +# This is a sample file distributed with Galaxy that is used to define a +# list of nucleotide BLAST databases, using three columns tab separated: # -#<unique_id> <database_caption> <base_name_path> +# <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. # -#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/ # -#So, for example, if your database is nt and the path to your base name -#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry -#would look like this: -# -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -# -#and your /depot/data2/galaxy/blastdb/nt directory would contain all of -#your "base names" (e.g.): +# 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. # -#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr -#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin -#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq -#...etc... +# For example, consider the NCBI partially non-redundant nucleotide +# nt BLAST database, where you have downloaded and decompressed the +# files under /data/blastdb/ meaning at the command line BLAST+ would +# would look at the files /data/blastdb/nt.n* when run with: # -#Your blastdb.loc file should include an entry per line for each "base name" -#you have stored. For example: +# $ blastn -db /data/blastdb/nt -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: +# +# nt{tab}NCBI partially non-redundant (nt){tab}/data/blastdb/nt # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test -#...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.loc file should include an entry per line for each +# version you have stored. For example: # -#You can download the NCBI provided protein databases like NT from here: -#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# nt_05Jun2010{tab}NCBI nt (partially non-redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nt +# nt_15Aug2010{tab}NCBI nt (partially non-redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nt +# ...etc... # -#See also blastdb_p.loc which is for any protein BLAST database, and -#blastdb_d.loc which is for any protein domains databases (like CDD). - - +# See also blastdb_p.loc which is for any protein BLAST database, and +# blastdb_d.loc which is for any protein domains databases (like CDD).
--- a/tool-data/blastdb_d.loc.sample Fri Jan 30 08:27:28 2015 -0500 +++ b/tool-data/blastdb_d.loc.sample Tue Mar 03 05:32:18 2015 -0500 @@ -1,35 +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): +# 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> # -#<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. +# +# You can download the NCBI provided databases as tar-balls from here: +# ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ # -#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. +# 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. # -#You can download the NCBI provided databases as tar-balls from here: -#ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ +# 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.*: # -#So, for example, if your database is CDD and the path to your base name -#is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this: -# -#Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd +# $ rpsblast -db /data/blastdb/domains/Cdd -query ... # -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/Cdd.*. +# 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: # -#Your blastdb_d.loc file should include an entry per line for each "base name" -#you have stored. For example: +# 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 NCBI CDD /data/blastdb/domains/Cdd -#Kog KOG (eukaryotes) /data/blastdb/domains/Kog -#Cog COG (prokaryotes) /data/blastdb/domains/Cog -#Pfam Pfam-A /data/blastdb/domains/Pfam -#Smart SMART /data/blastdb/domains/Smart -#Tigr TIGR /data/blastdb/domains/Tigr -#Prk Protein Clusters database /data/blastdb/domains/Prk -#...etc... +# 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... # -#See also blastdb.loc which is for any nucleotide BLAST database, and -#blastdb_p.loc which is for any protein BLAST databases. +# 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.
--- a/tool-data/blastdb_p.loc.sample Fri Jan 30 08:27:28 2015 -0500 +++ b/tool-data/blastdb_p.loc.sample Tue Mar 03 05:32:18 2015 -0500 @@ -1,30 +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 -#(longer whitespace are TAB characters): +# 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> <database_caption> <base_name_path> +# <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. # -#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/ # -#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 +# 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. # -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. +# 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*: # -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: +# $ 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 # -#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... +# 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: # -#You can download the NCBI provided protein databases like NR from here: -#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# 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). +# See also blastdb.loc which is for any nucleotide BLAST database, and +# blastdb_d.loc which is for any protein domains databases (like CDD).
--- a/tools/ncbi_blast_plus/README.rst Fri Jan 30 08:27:28 2015 -0500 +++ b/tools/ncbi_blast_plus/README.rst Tue Mar 03 05:32:18 2015 -0500 @@ -19,6 +19,9 @@ These wrappers are available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus +In-development test releases are available from the Test Tool Shed at: +http://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ + Citation ========
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Fri Jan 30 08:27:28 2015 -0500 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Tue Mar 03 05:32:18 2015 -0500 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> - <repository changeset_revision="236046d1d441" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="da92fef90117" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>