Mercurial > repos > devteam > data_manager_twobit_builder
view tool-data/alignseq.loc.sample @ 3:e697ffc1197e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 984fd87f7bb30469ac078cf32d2cbb42e62c11dd
author | iuc |
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date | Fri, 09 Jun 2017 05:25:37 -0400 |
parents | 26e3ae5f74ed |
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#This is a sample file distributed with Galaxy that enables tools #to use alignment data stored as axt files (lines starting with "align") #or nib files (lines starting with "seq"). You will need to index #them and then create an alignseq.loc file similar to this one (store #it in this directory) that points to the directories in which those #alignments are stored. The "align" data referred to by the alignseq.loc #file has this format (white space characters are TAB characters): # #align <build1> <build2> <dir> # #So, for example, if you had hg18/bosTau2 alignment files stored in #/depot/data2/galaxy/hg18/align/bosTau2, then the alignseq.loc entry #would look like this: # #align hg18 bosTau2 /depot/data2/galaxy/hg18/align/bosTau2 # #and your /depot/data2/galaxy/hg18/align/bosTau2 directory would #contain all of your alignment files (e.g.): # #-rw-rw-r-- 1 nate galaxy 151842783 2006-01-08 01:00 chr10.axt #-rw-rw-r-- 1 nate galaxy 79575 2006-01-08 01:00 chr10_random.axt #-rw-rw-r-- 1 nate galaxy 155015634 2006-01-08 01:01 chr11.axt #...etc... # #Your alignseq.loc file should include an entry per line for each alignment #file you have stored. For example: # #align anoGam1 dm1 /depot/data2/galaxy/anoGam1/align/dm1 #align anoGam1 dm2 /depot/data2/galaxy/anoGam1/align/dm2 #align canFam1 hg17 /depot/data2/galaxy/canFam1/align/hg17 #...etc... # #The "seq" data referred to by the alignseq.loc file has this #format (white space characters are TAB characters): # #seq <build1> <dir> # #So, for example, if you had anoGam1 sequence files stored in #/depot/data2/galaxy/anoGam1/seq, then the alignseq.loc entry #would look like this: # #seq anoGam1 /depot/data2/galaxy/anoGam1/seq #and your seq anoGam1 /depot/data2/galaxy/anoGam1/seq directory would #contain all of your sequence files (e.g.): # #-rw-rw-r-- 1 nate galaxy 24397551 2006-06-26 12:51 chr2L.nib #-rw-rw-r-- 1 nate galaxy 31362964 2006-06-26 12:51 chr2R.nib #-rw-rw-r-- 1 nate galaxy 20642013 2006-06-26 12:51 chr3L.nib #-rw-rw-r-- 1 nate galaxy 26636071 2006-06-26 12:51 chr3R.nib # #Your alignseq.loc file should include an entry per line for each sequence #file you have stored. For example: # #seq anoGam1 /depot/data2/galaxy/anoGam1/seq #seq bosTau2 /depot/data2/galaxy/bosTau2/seq #seq bosTau3 /depot/data2/galaxy/bosTau3/seq #...etc...