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annotate tool-data/gottcha_indices.loc.sample @ 6:1b81bee6080f draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 9931b6d7fbe3c7e3220ee01f7fd063897891a5c6-dirty
author jdv
date Mon, 30 Jan 2017 22:07:43 -0500
parents 2569a83977f5
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2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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1 # gottcha_indices.loc.sample
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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3 # to use a directory of indexed data files. This one is for GOTTCHA.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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5 # First create these data files and save them in your own data directory structure.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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6 # Then, create a bowtie_indices.loc file to use those indexes with tools.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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7 # Copy this file, save it with the same name (minus the .sample),
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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8 # follow the format examples, and store the result in this directory.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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9 # The file should include an one line entry for each index set.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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10 # The path points to the "basename" for the set, not a specific file.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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11 # It has three text columns seperated by TABS.
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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12 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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13 # <unique_id> <display_name> <file_base_path>
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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14 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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15 # So, for example, if you had pre-built indices stored in:
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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16 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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17 # /depot/data2/galaxy/gottcha/
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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18 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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19 # containing GOTTCHA index files, such as:
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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20 # -rw-r--r-- 1 root root 21M Sep 15 2015 classLookupByOrder.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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21 # -rw-r--r-- 1 root root 30M Sep 15 2015 familyLookupByGenus.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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22 # -rw-r--r-- 1 root root 7.8M Sep 15 2015 genomeVitals.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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23 # -rw-r--r-- 1 root root 73M Sep 15 2015 genusLookupBySpecies.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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24 # -rw-r--r-- 1 root root 27M Sep 15 2015 orderLookupByFamily.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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25 # -rw-r--r-- 1 root root 21M Sep 15 2015 phylumLookupByClass.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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26 # -rw-r--r-- 1 root root 268M Sep 15 2015 speciesTreeGI.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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27 # -rw-r--r-- 1 root root 176M Sep 15 2015 taxLookupBySpecies.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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28 # -rw-r--r-- 1 root root 82M Sep 15 2015 variantSpeciesLookup.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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29 # -rw-r--r-- 1 root root 16M Sep 15 2015 variantStrainLookup.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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30 # -rw-r--r-- 1 root root 4.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.bwt
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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31 # -rw-r--r-- 1 root root 1.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.pac
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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32 # -rw-r--r-- 1 root root 2.0G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.ann
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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33 # -rw-r--r-- 1 root root 22 Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.amb
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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34 # -rw-r--r-- 1 root root 2.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.sa
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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35 # -rw-r--r-- 1 root root 98M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.bwt
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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36 # -rw-r--r-- 1 root root 25M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.pac
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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37 # -rw-r--r-- 1 root root 25M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.ann
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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38 # -rw-r--r-- 1 root root 19 Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.amb
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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39 # -rw-r--r-- 1 root root 49M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.sa
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
jdv
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40 # -rw-r--r-- 1 root root 16M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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41 # -rw-r--r-- 1 root root 1.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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42 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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43 # then the gottcha_indices.loc entries could look like this:
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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44 #
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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45 #bacteria_v20150825 Bacteria /depot/data2/galaxy/gottcha/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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46 #viruses_v20150825 Viruses /depot/data2/galaxy/gottcha/GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species
2569a83977f5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
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47 #