Mercurial > repos > jdv > gottcha
comparison tool-data/gottcha_indices.loc.sample @ 0:2569a83977f5 draft
planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
| author | jdv |
|---|---|
| date | Mon, 30 Jan 2017 19:07:21 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:2569a83977f5 |
|---|---|
| 1 # gottcha_indices.loc.sample | |
| 2 # This is a *.loc.sample file distributed with Galaxy that enables tools | |
| 3 # to use a directory of indexed data files. This one is for GOTTCHA. | |
| 4 # See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup | |
| 5 # First create these data files and save them in your own data directory structure. | |
| 6 # Then, create a bowtie_indices.loc file to use those indexes with tools. | |
| 7 # Copy this file, save it with the same name (minus the .sample), | |
| 8 # follow the format examples, and store the result in this directory. | |
| 9 # The file should include an one line entry for each index set. | |
| 10 # The path points to the "basename" for the set, not a specific file. | |
| 11 # It has three text columns seperated by TABS. | |
| 12 # | |
| 13 # <unique_id> <display_name> <file_base_path> | |
| 14 # | |
| 15 # So, for example, if you had pre-built indices stored in: | |
| 16 # | |
| 17 # /depot/data2/galaxy/gottcha/ | |
| 18 # | |
| 19 # containing GOTTCHA index files, such as: | |
| 20 # -rw-r--r-- 1 root root 21M Sep 15 2015 classLookupByOrder.dmp | |
| 21 # -rw-r--r-- 1 root root 30M Sep 15 2015 familyLookupByGenus.dmp | |
| 22 # -rw-r--r-- 1 root root 7.8M Sep 15 2015 genomeVitals.dmp | |
| 23 # -rw-r--r-- 1 root root 73M Sep 15 2015 genusLookupBySpecies.dmp | |
| 24 # -rw-r--r-- 1 root root 27M Sep 15 2015 orderLookupByFamily.dmp | |
| 25 # -rw-r--r-- 1 root root 21M Sep 15 2015 phylumLookupByClass.dmp | |
| 26 # -rw-r--r-- 1 root root 268M Sep 15 2015 speciesTreeGI.dmp | |
| 27 # -rw-r--r-- 1 root root 176M Sep 15 2015 taxLookupBySpecies.dmp | |
| 28 # -rw-r--r-- 1 root root 82M Sep 15 2015 variantSpeciesLookup.dmp | |
| 29 # -rw-r--r-- 1 root root 16M Sep 15 2015 variantStrainLookup.dmp | |
| 30 # -rw-r--r-- 1 root root 4.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.bwt | |
| 31 # -rw-r--r-- 1 root root 1.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.pac | |
| 32 # -rw-r--r-- 1 root root 2.0G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.ann | |
| 33 # -rw-r--r-- 1 root root 22 Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.amb | |
| 34 # -rw-r--r-- 1 root root 2.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.sa | |
| 35 # -rw-r--r-- 1 root root 98M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.bwt | |
| 36 # -rw-r--r-- 1 root root 25M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.pac | |
| 37 # -rw-r--r-- 1 root root 25M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.ann | |
| 38 # -rw-r--r-- 1 root root 19 Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.amb | |
| 39 # -rw-r--r-- 1 root root 49M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.sa | |
| 40 # -rw-r--r-- 1 root root 16M Sep 21 2015 GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp | |
| 41 # -rw-r--r-- 1 root root 1.1G Sep 21 2015 GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species.parsedGOTTCHA.dmp | |
| 42 # | |
| 43 # then the gottcha_indices.loc entries could look like this: | |
| 44 # | |
| 45 #bacteria_v20150825 Bacteria /depot/data2/galaxy/gottcha/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species | |
| 46 #viruses_v20150825 Viruses /depot/data2/galaxy/gottcha/GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species | |
| 47 # |