# HG changeset patch
# User iuc
# Date 1478356664 14400
# Node ID 2f9619adab912d9e60a9116ded25066558547c7a
# Parent  b573ecb2ca66dac76c4d4a26d9489ccf001ec866
planemo upload commit 76744a97a6f837ee60104321867e6451fec78d74-dirty

diff -r b573ecb2ca66 -r 2f9619adab91 tool-data/blastdb_d.loc.sample
--- 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.
diff -r b573ecb2ca66 -r 2f9619adab91 tool-data/blastdb_p.loc.sample
--- /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).