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author dchristiany
date Mon, 28 Oct 2019 06:53:13 -0400
parents 238a5328279d
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1 # Copyright (C) 2014 INRA
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2 #
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3 # This program is free software: you can redistribute it and/or modify
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4 # it under the terms of the GNU General Public License as published by
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5 # the Free Software Foundation, either version 3 of the License, or
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6 # (at your option) any later version.
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7 #
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8 # This program is distributed in the hope that it will be useful,
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9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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11 # GNU General Public License for more details.
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12 #
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13 # You should have received a copy of the GNU General Public License
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14 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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15 #
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16 #
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17 #This is a sample file that enables tools FROGS_filters to identify phix contaminant. You will #need to create or download Blast+ index.
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18 #download link : http://genoweb.toulouse.inra.fr/frogs_databanks/contaminants
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19 #Finally you will need to create phiX_db.loc file similar to this one in your galaxy
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20 #tool-data directory.The phiX_db.loc file has this format (longer white space characters are
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21 #TAB characters):
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22 #
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23 #<contaminant_name> <name> <file_path>
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24 #
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25 #First column will be the visible name in galaxy.
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26 #So, for example, if you had phix indexed stored in
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27 #/galaxy_databanks/phiX/
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28 #then the phiX_db.loc entry would look like this:
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29 #
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30 #
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31 # EXAMPLE FOR TEST :
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32 #phiX_test phiX_test ${__HERE__}/phiX_db_data/phi.fa
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33 #
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34 #and your /galaxy_databanks/phiX/ directory
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35 #would contain index files:
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36 #
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37 #-rwxrwxr-x 1 gpascal FROGS 5535 16 sept. 2015 phi.fa
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38 #-rw-rwxr-- 1 gpascal FROGS 132 16 sept. 2015 phi.fa.nhr
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39 #-rw-rwxr-- 1 gpascal FROGS 88 16 sept. 2015 phi.fa.nin
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40 #-rw-rwxr-- 1 gpascal FROGS 1348 16 sept. 2015 phi.fa.nsq
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41 #