Mercurial > repos > devteam > data_manager_twobit_builder
diff tool-data/alignseq.loc.sample @ 0:74b09c8e5f6e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_twobit_builder commit 130cb0c08ad3c5b858ba46b1024dcdccc3cb68c6-dirty
| author | devteam |
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| date | Thu, 11 Jun 2015 16:14:27 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/alignseq.loc.sample Thu Jun 11 16:14:27 2015 -0400 @@ -0,0 +1,57 @@ +#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...