commit/galaxy-central: richard_burhans: remove Genome Diversity {test, tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0ffa2695e436/ changeset: 0ffa2695e436 user: richard_burhans date: 2012-04-09 22:34:51 summary: remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository affected #: 10 files diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_flanking_dna.txt --- a/test-data/gd.extract_flanking_dna.txt +++ /dev/null @@ -1,40 +0,0 @@ -SEQUENCE_ID=chr18_57379354_57380496 315 C T -SEQUENCE_TEMPLATE=CTCTCTGATGAGCAAGGAGCAGCTCTGATTGGGATCGCCAAGGAGCTGGAATCGGCCCTGGGTGTCTGTGTCCACGTCCTGACCTGGCTTGTTGGTGGCCACTGGCAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACTCCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCACCATCACAAACTCCTGCATCTGCAGCTTGAATGAGTCCAGAGCCTGAGACCCTATGAGGGAGACAGAGGTTCAAGCTGCAAGCCCAGCCCAGACCACCCCCCCCAGCCCCCGGGCCCCTCCTGGCCACCCCCTTCCACTCACCGCCCCACAGCATGGCCAAGAACAGTGGCAGGAACA -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr18_48070585_48071386 514 C T -SEQUENCE_TEMPLATE=GCCCTCCCCTGCCCAGTCCCTCAGCCCCTGCCTCCTCGTGCAGGCAGGCCTCCAGGATCTGCAGGCCAGACCTCCAGAAGGCCTTGTTCATGGCATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCACCCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTCTTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCCTGGGGAGACAGAGGTAGGAAGTGCCTTTGATGACCCTGAATATGGGGCACAGCACCTTCAAGAGCAGAGGGTACACATCTCAGTTGACACTAGGTTGGGGGACACACGCCTATGAGAGGCCTTGGTTT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr14_80021455_80022064 138 G A -SEQUENCE_TEMPLATE=ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG -SEQUENCE_TARGET=133,11 -= -SEQUENCE_ID=chr19_39866997_39874915 3117 C T -SEQUENCE_TEMPLATE=CCCAGCCAGAGAGGCCCTGGGGGCTGCGGCTACTCTGGCCCCCTTCCTTGCCTGAACAGTGCTTTGCTGGCCCCCGGGAGCCAGAGGGCACAGTCTCTTGGTGGTAGAGGAGGCCTGTGGCAAGGAAGCAGGCTCCGGGGGTGTCTCTTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAGCGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGCTGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTTGAGGAAGCCTGTGAGGGGTGGGATGGTGGGTGGTGGATAGAGCCCCGGGCTTGGCAGAAGCACACTCTCCCCTACCATCCCTAG -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr15_64470252_64471048 89 G A -SEQUENCE_TEMPLATE=TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT -SEQUENCE_TARGET=84,11 -= -SEQUENCE_ID=chr18_50154905_50155664 304 A G -SEQUENCE_TEMPLATE=GGTACCTTGGTTTCTCTGTCAAGAGACCTATGTGTTGACTGTCATCACTGTACCATGGTCGGGGGGTGGTCGGGAGGAGCCAGATGTGGGTCTGAATGAACATGTGGCGTTCTTGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAGTGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGCACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCGCCTCAGTCCTCCTCATCCATCCCTCCCGGGTCCCGTGGTGCTGGGGGATGGGTCCTCCCAGGCTGCCTCCCCTCTGAGGGGCTCTTCCCCCACACAGGGCCGGGCATTT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr2_75111355_75112576 314 A C -SEQUENCE_TEMPLATE=TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr8_93901796_93905612 2471 A C -SEQUENCE_TEMPLATE=GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr10_7434473_7435447 524 T C -SEQUENCE_TEMPLATE=ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr19_14240610_14242055 232 C T -SEQUENCE_TEMPLATE=CAACATTGTAAAGTAATTATACTCCAATTAAAAAACACAGTGATATCAAAGATGATTTCCAATACTAAAATCTATCTCCAAGAATTTACAGCTTTGAAGAAAATTTTACAATCTCCGGAATTCATGTTAATATTGAAACAACATTTCTGTCCTAATTATTTATTGGAACCTCTTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGACGGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACTTTCGGAGAGGAAAACAGGAAGAGGATGACCAATAGCTATTTGAAAAGAGCTGAGAACTCTAGAATCACCCAAGCGACGTGTGCACTGTTAAATTCTGGAGGGGGTTTGATCAAAGCGGAGATTG -SEQUENCE_TARGET=196,11 -= diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_primers.txt --- a/test-data/gd.extract_primers.txt +++ /dev/null @@ -1,119 +0,0 @@ -> chr18_57379354_57380496 315 C T 0.014036 - BanI - 1 CAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACT - >>>>>>>>>>>>>>>>>>>> - - 61 CCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCAC - - -121 CATCACAAACTCCTGCATCTGCAGC - <<<<<<<<<<<<<<<<<<<< - -> chr18_48070585_48071386 514 C T 0.163186 - - 1 ATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCAC - >>>>>>>>>>>>>>>>>>>> - - 61 CCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTC - - -121 TTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCC - <<<<< - -181 TGGGGAGACAGAGGTAGG - <<<<<<<<<<<<<<< - -> chr14_80021455_80022064 138 G A 0.194886 - Hsp92II - 1 CGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCT - >>>>>>>>>>>>>>>>>>>> - - 61 TGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGC - <<<<<<<<<<<<< - -121 GTAGTGCAAA - <<<<<<< - -> chr19_39866997_39874915 3117 C T 0.946156 - BstOI - 1 TTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAG - >>>>>>>>>>>>>>>>>>>> - - 61 CGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGC - - -121 TGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTT - <<<<<<<<<<<<<<<<<<<< - -> chr15_64470252_64471048 89 G A 1.325099 - - 1 GTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTC - >>>>>>>>>>>>>>>>>>>> - - 61 AGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGG - - -121 GCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGAT - <<<<<< - -181 GCATCGCTCTCTTCCAC - <<<<<<<<<<<<<< - -> chr18_50154905_50155664 304 A G 0.578070 - - 1 TGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAG - >>>>>>>>>>>>>>>>>>>> - - 61 TGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGC - - -121 ACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCG - - -181 CCTCAGTCCTCCTCATCCATCCCTC - <<<<<<<<<<<<<<<<<<<< - -> chr2_75111355_75112576 314 A C 0.613831 - - 1 TTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGC - >>>>>>>>>>>>>>>>>>>> - - 61 AAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAA - - -121 CAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACAT - - -181 GATCAGGGGCAAGTTCTATTGGATA - <<<<<<<<<<<<<<<<<<<< - -> chr8_93901796_93905612 2471 A C 0.322555 - MboI,Sau3AI - 1 GGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATn - >>>>>>>>>>>>>>>>>>>> - - 61 GCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAG - <<<<<<<<<<<<<<<<<<<< - -121 C - - -> chr10_7434473_7435447 524 T C 1.119264 - - 1 CCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACA - >>>>>>>>>>>>>>>>>>>> - - 61 AATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGA - - -121 CAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAAT - <<<<<<<<<<<<<<<<<<<< - -> chr19_14240610_14242055 232 C T 0.835026 - - 1 TTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGAC - >>>>>>>>>>>>>>>>>>>> - - 61 GGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACT - <<<<<<<<<<<<<<<<<<<< - diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.sample.wsf --- a/test-data/gd.sample.wsf +++ /dev/null @@ -1,12 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 -chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 -chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 -chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 -chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 -chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0 -chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0 -chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 -chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 -chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_restriction_enzymes.wsf --- a/test-data/gd.select_restriction_enzymes.wsf +++ /dev/null @@ -1,5 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 -chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 -chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_snps.wsf --- a/test-data/gd.select_snps.wsf +++ /dev/null @@ -1,7 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 -chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 -chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 -chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 -chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ /dev/null @@ -1,22 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of sequence length files. You will need to create these -# sequence length files and then create a gd.chrlens.loc file similar to -# this one (store it in this directory) that points to the directories -# in which these sequence length files are stored. The gd.chrlens.loc -# file has the following format (white space characters are TAB -# characters): -# -#<species><reference_species_file_path> -# -# So, for example, if you used Monodelphis domestica as the reference -# species for a collection of Sarcophilus harrisii SNPs, then the -# gd.chrlens.loc entry would look like this: -# -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt -# -# Your gd.chrlens.loc file should include an entry for each pair of -# species SNPs and reference species. For example: -# -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ /dev/null @@ -1,22 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of primers files. You will need to create these primers -# files and then create a gd.primers.loc file similar to this one (store -# it in this directory) that points to the directories in which these -# primers files are stored. The gd.primers.loc file has the following -# format (white space characters are TAB characters): -# -#<species><primers_file_path> -# -# So, for example, if you had a primers file located at -# /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of -# Ovis canadensis SNPs, then the gd.primers.loc entry would look like -# this: -# -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -# -# Your gd.primers.loc file should include an entry for each pair of -# species SNPs and primers file. For example: -# -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.restriction_enzymes.txt.sample --- a/tool-data/gd.restriction_enzymes.txt.sample +++ /dev/null @@ -1,99 +0,0 @@ -Acc65I - GGTACC Acc65I -AccB7I - CCANNNNNTGG AccB7I -AccI - GT(A/C)(G/T)AC AccI -AccIII - TCCGGA AccIII -AcyI - G(A/G)CG(C/T)C AcyI -AgeI - ACCGGT AgeI -AluI - AGCT AluI -Alw44I - GTGCAC Alw44I -ApaI - GGGCCC ApaI -AvaI - C(C/T)CG(A/G)G AvaI -AvaII - GG(A/T)CC AvaII -BalI - TGGCCA BalI -BamHI - GGATCC BamHI -BanI - GG(C/T)(A/G)CC BanI -BanII - G(A/G)GC(C/T)C BanII -BbuI - GCATGC BbuI -BclI - TGATCA BclI -BglI - GCCNNNNNGGC BglI -BglII - AGATCT BglII -BsaMI - GAATGC BsaMI -BsaOI - CG(A/G)(C/T)CG BsaOI -Bsp1286I - G(A/G/T)GC(A/C/T)C Bsp1286I -BsrBRI - GATNNNNATC BsrBRI -BsrSI - ACTGG BsrSI -BssHII - GCGCGC BssHII -Bst98I - CTTAAG Bst98I -BstEII - GGTNACC BstEII -BstOI - CC(A/T)GG BstOI -BstXI - CCANNNNNNTGG BstXI -BstZI - CGGCCG BstZI -Bsu36I - CCTNAGG Bsu36I -CfoI - GCGC CfoI -ClaI - ATCGAT ClaI -Csp45I - TTCGAA Csp45I -CspI - CGG(A/T)CCG CspI -DdeI - CTNAG DdeI -DpnI - GATC DpnI -DraI - TTTAAA DraI -EclHKI - GACNNNNNGTC EclHKI -Eco47III - AGCGCT Eco47III -Eco52I - CGGCCG Eco52I -Eco72I - CACGTG Eco72I -EcoRI - GAATTC EcoRI -EcoRV - GATATC EcoRV -HaeII - (A/G)GCGC(C/T) HaeII -HaeIII - GGCC HaeIII -HhaI - GCGC HhaI -HincII - GT(C/T)(A/G)AC HincII -HindIII - AAGCTT HindIII -HinfI - GANTC HinfI -HpaI - GTTAAC HpaI -HpaII - CCGG HpaII -Hsp92I - G(A/G)CG(C/T)C Hsp92I -Hsp92II - CATG Hsp92II -I-PpoI - TAACTATGACTCTCTTAAGGTAGCCAAAT I-PpoI -KpnI - GGTACC KpnI -MboI - GATC MboI -MluI - ACGCGT MluI -MspA1I - C(A/C)GC(G/T)G MspA1I -MspI - CCGG MspI -NaeI - GCCGGC NaeI -NarI - GGCGCC NarI -NciI - CC(C/G)GG NciI -NcoI - CCATGG NcoI -NdeI - CATATG NdeI -NgoMIV - GCCGGC NgoMIV -NheI - GCTAGC NheI -NotI - GCGGCCGC NotI -NruI - TCGCGA NruI -NsiI - ATGCAT NsiI -PstI - CTGCAG PstI -PvuI - CGATCG PvuI -PvuII - CAGCTG PvuII -RsaI - GTAC RsaI -SacI - GAGCTC SacI -SacII - CCGCGG SacII -SalI - GTCGAC SalI -Sau3AI - GATC Sau3AI -Sau96I - GGNCC Sau96I -ScaI - AGTACT ScaI -SfiI - GGCCNNNNNGGCC SfiI -SgfI - GCGATCGC SgfI -SinI - GG(A/T)CC SinI -SmaI - CCCGGG SmaI -SnaBI - TACGTA SnaBI -SpeI - ACTAGT SpeI -SphI - GCATGC SphI -SspI - AATATT SspI -StuI - AGGCCT StuI -StyI - CC(A/T)(A/T)GG StyI -TaqI - TCGA TaqI -Tru9I - TTAA Tru9I -Tth111I - GACNNNGTC Tth111I -VspI - ATTAAT VspI -XbaI - TCTAGA XbaI -XhoI - CTCGAG XhoI -XhoII - (A/G)GATC(C/T) XhoII -XmaI - CCCGGG XmaI -XmnI - GAANNNNTTC XmnI diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ /dev/null @@ -1,21 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of SNP call files. You will need to create these SNP -# call files and then create a gd.snps.loc file similar to this one (store -# it in this directory) that points to the directories in which these -# SNP call files are stored. The gd.snps.loc file has the following -# format (white space characters are TAB characters): -# -#<species><SNP_call_file_path> -# -# So, for example, if you had a SNP call file located at -# /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of -# Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: -# -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -# -# Your gd.snps.loc file should include an entry for each pair of species -# SNPs and SNP call file. For example: -# -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.species.txt.sample --- a/tool-data/gd.species.txt.sample +++ /dev/null @@ -1,3 +0,0 @@ -# genome diversity species -tasmanian_devil Tasmanian devil -bighorn bighorn Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
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