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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Tue, 08 Aug 2017 12:55:09 -0400
parents 22a767177ac9
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #NOTE: This file comes from the tool galaxyp/blast_plus_remote_blastp
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22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
galaxyp
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2 # This is a sample file distributed with Galaxy that is used to define a
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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3 # list of protein BLAST databases, using three columns tab separated:
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4 #
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22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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5 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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6 #
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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7 # The captions typically contain spaces and might end with the build date.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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8 # It is important that the actual database name does not have a space in
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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9 # it, and that there are only two tabs on each line.
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10 #
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22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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11 # You can download the NCBI provided protein databases like NR from here:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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12 # ftp://ftp.ncbi.nlm.nih.gov/blast/db/
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13 #
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22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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14 # For simplicity, many Galaxy servers are configured to offer just a live
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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15 # version of each NCBI BLAST database (updated with the NCBI provided
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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16 # Perl scripts or similar). In this case, we recommend using the case
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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17 # sensistive base-name of the NCBI BLAST databases as the unique id.
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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18 # Consistent naming is important for sharing workflows between Galaxy
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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19 # servers.
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20 #
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21 # For example, consider the NCBI "non-redundant" protein BLAST database
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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22 # where you have downloaded and decompressed the files under /data/blastdb/
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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23 # meaning at the command line BLAST+ would be run with something like
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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24 # which would look at the files /data/blastdb/nr.p*:
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25 #
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22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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26 # $ blastp -db /data/blastdb/nr -query ...
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27 #
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28 # In this case use nr (lower case to match the NCBI file naming) as the
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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29 # unique id in the first column of blastdb_p.loc, giving an entry like
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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30 # this:
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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31 #
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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32 # nr{tab}NCBI non-redundant (nr){tab}/data/blastdb/nr
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33 #
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34 # Alternatively, rather than a "live" mirror of the NCBI databases which
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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35 # are updated automatically, for full reproducibility the Galaxy Team
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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36 # recommend saving date-stamped copies of the databases. In this case
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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37 # your blastdb_p.loc file should include an entry per line for each
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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38 # version you have stored. For example:
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39 #
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40 # nr_05Jun2010{tab}NCBI NR (non redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nr
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41 # nr_15Aug2010{tab}NCBI NR (non redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nr
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42 # ...etc...
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43 #
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44 # See also blastdb.loc which is for any nucleotide BLAST database, and
22a767177ac9 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 8cb8939dadaad8e804e35128cfb7b2560eb4d9b4
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45 # blastdb_d.loc which is for any protein domains databases (like CDD).