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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 0331dc2148913e04c90481cb08d38b8bfaed5e6a
author iuc
date Mon, 04 Dec 2023 21:40:52 +0000
parents e6799e98c5fb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
iuc
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1 # This is a sample file distributed with Galaxy that is used to define a
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
iuc
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2 # list of nucleotide BLAST databases, using three columns tab separated:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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3 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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4 # <unique_id>{tab}<database_caption>{tab}<base_name_path>
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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5 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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6 # The captions typically contain spaces and might end with the build date.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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7 # It is important that the actual database name does not have a space in
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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8 # it, and that there are only two tabs on each line.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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9 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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10 # You can download the NCBI provided protein databases like NR from here:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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11 # ftp://ftp.ncbi.nlm.nih.gov/blast/db/
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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12 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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13 # For simplicity, many Galaxy servers are configured to offer just a live
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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14 # version of each NCBI BLAST database (updated with the NCBI provided
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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15 # Perl scripts or similar). In this case, we recommend using the case
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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16 # sensistive base-name of the NCBI BLAST databases as the unique id.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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17 # Consistent naming is important for sharing workflows between Galaxy
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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18 # servers.
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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19 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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20 # For example, consider the NCBI partially non-redundant nucleotide
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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21 # nt BLAST database, where you have downloaded and decompressed the
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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22 # files under /data/blastdb/ meaning at the command line BLAST+ would
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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23 # would look at the files /data/blastdb/nt.n* when run with:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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24 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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25 # $ blastn -db /data/blastdb/nt -query ...
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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26 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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27 # In this case use nr (lower case to match the NCBI file naming) as the
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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28 # unique id in the first column of blastdb_p.loc, giving an entry like
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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29 # this:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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30 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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31 # nt{tab}NCBI partially non-redundant (nt){tab}/data/blastdb/nt
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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32 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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33 # Alternatively, rather than a "live" mirror of the NCBI databases which
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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34 # are updated automatically, for full reproducibility the Galaxy Team
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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35 # recommend saving date-stamped copies of the databases. In this case
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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36 # your blastdb.loc file should include an entry per line for each
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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37 # version you have stored. For example:
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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38 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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39 # nt_05Jun2010{tab}NCBI nt (partially non-redundant) 05 Jun 2010{tab}/data/blastdb/05Jun2010/nt
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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40 # nt_15Aug2010{tab}NCBI nt (partially non-redundant) 15 Aug 2010{tab}/data/blastdb/15Aug2010/nt
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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41 # ...etc...
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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42 #
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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43 # See also blastdb_p.loc which is for any protein BLAST database, and
e6799e98c5fb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast commit 15fc6c06f743bae276ff02dc405e7da61a07bd08"
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44 # blastdb_d.loc which is for any protein domains databases (like CDD).