#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 # #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 # #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... seq hg19_rCRS_pUC18_phiX174 /cvmfs/data.galaxyproject.org/managed/seq/hg19_rCRS_pUC18_phiX174.2bit seq rn6 /cvmfs/data.galaxyproject.org/managed/seq/rn6.2bit seq dm6 /cvmfs/data.galaxyproject.org/managed/seq/dm6.2bit seq musFur1 /cvmfs/data.galaxyproject.org/managed/seq/musFur1.2bit seq nomLeu3 /cvmfs/data.galaxyproject.org/managed/seq/nomLeu3.2bit seq cerSim1 /cvmfs/data.galaxyproject.org/managed/seq/cerSim1.2bit seq danRer10 /cvmfs/data.galaxyproject.org/managed/seq/danRer10.2bit seq papAnu2 /cvmfs/data.galaxyproject.org/managed/seq/papAnu2.2bit seq bosTau8 /cvmfs/data.galaxyproject.org/managed/seq/bosTau8.2bit seq melUnd1 /cvmfs/data.galaxyproject.org/managed/seq/melUnd1.2bit seq allMis1 /cvmfs/data.galaxyproject.org/managed/seq/allMis1.2bit seq vicPac1 /cvmfs/data.galaxyproject.org/managed/seq/vicPac1.2bit seq vicPac2 /cvmfs/data.galaxyproject.org/managed/seq/vicPac2.2bit seq gadMor1 /cvmfs/data.galaxyproject.org/managed/seq/gadMor1.2bit seq dasNov3 /cvmfs/data.galaxyproject.org/managed/seq/dasNov3.2bit seq panPan1 /cvmfs/data.galaxyproject.org/managed/seq/panPan1.2bit seq felCat8 /cvmfs/data.galaxyproject.org/managed/seq/felCat8.2bit seq aptMan1 /cvmfs/data.galaxyproject.org/managed/seq/aptMan1.2bit seq bosTau7 /cvmfs/data.galaxyproject.org/managed/seq/bosTau7.2bit seq apiMel4 /cvmfs/data.galaxyproject.org/managed/seq/apiMel4.2bit seq Amel_4.5 /cvmfs/data.galaxyproject.org/managed/seq/Amel_4.5.2bit