Mercurial > repos > sarahinraauzeville > rnaseq_tophat2

comparison tophat_indexes.loc @ 0:15aa80493a82 draft

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author sarahinraauzeville
date Thu, 11 Feb 2016 08:45:06 -0500
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1 #This is a sample file distributed with Galaxy that enables tools
2 #to use a directory of Bowtie indexed sequences data files. You will
3 #need to create these data files and then create a bowtie_indices.loc
4 #file similar to this one (store it in this directory) that points to
5 #the directories in which those files are stored. The bowtie_indices.loc
6 #file has this format (longer white space characters are TAB characters):
7 #
8 #<unique_build_id> <dbkey> <display_name> <file_base_path>
9 #
10 #So, for example, if you had hg18 indexed stored in
11 #/depot/data2/galaxy/bowtie/hg18/,
12 #then the bowtie_indices.loc entry would look like this:
13 #
14 #hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
15 #
16 #and your /depot/data2/galaxy/bowtie/hg18/ directory
17 #would contain hg18.*.ebwt files:
18 #
19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
22 #...etc...
23 #
24 #Your bowtie_indices.loc file should include an entry per line for each
25 #index set you have stored. The "file" in the path does not actually
26 #exist, but it is the prefix for the actual index files. For example:
27 #
28 #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
29 #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
30 #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
31 #...etc...
32 #
33
34 #Banques temporaires mises en place au debut de l installation de Galaxy
35 #AthalianaAllChr AthalianaAllChr AthalianaAllChr /path/to/bank/bowtiedb/AthalianaAllChr
36 #Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster All Chr /path/to/bank/bowtiedb/Drosophila_melanogaster_AllChr
37 #Homo_sapiens_AllChr Homo_sapiens_AllChr Homo_sapiens_AllChr /path/to/bank/bowtiedb/Homo_sapiens_AllChr
38 #yeast.nt yeast.nt yeast nt /path/to/bank/bowtiedb/yeast.nt
39
40 #Banques definitives transmises par l administrateur system sur /path/to/bank/bowtiedb
41 Arabidopsis_thaliana Arabidopsis_thaliana Arabidopsis thaliana /path/to/bank/bowtie2db/Arabidopsis_thaliana
42 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865 Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865
43 Capra_hircus Capra_hircus Capra_hircus /path/to/bank/bowtie2db/Capra_hircus
44 Danio_rerio_Zv9_62_chr_22 Danio_rerio_Zv9_62_chr_22 Danio rerio Zv9 62 chr 22 /path/to/bank/bowtie2db/Danio_rerio.Zv9.62
45 Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster AllChr /path/to/bank/bowtie2db/Drosophila_melanogaster_AllChr
46 ensembl_bos_taurus_genome ensembl_bos_taurus_genome ensembl bos taurus genome /path/to/bank/bowtie2db/ensembl_bos_taurus_genome
47 ensembl_danio_rerio_genome ensembl_danio_rerio_genome ensembl danio rerio genome /path/to/bank/bowtie2db/ensembl_danio_rerio_genome
48 ensembl_equus_caballus_genome ensembl_equus_caballus_genome ensembl equus caballus genome /path/to/bank/bowtie2db/ensembl_equus_caballus_genome
49 ensembl_gallus_gallus_genome ensembl_gallus_gallus_genome ensembl gallus gallus genome /path/to/bank/bowtie2db/ensembl_gallus_gallus_genome
50 ensembl_homo_sapiens_genome ensembl_homo_sapiens_genome ensembl homo sapiens genome /path/to/bank/bowtie2db/ensembl_homo_sapiens_genome
51 ensembl_mus_musculus_genome ensembl_mus_musculus_genome ensembl mus musculus genome /path/to/bank/bowtie2db/ensembl_mus_musculus_genome
52 ensembl_oreochromis_niloticus_genome ensembl_oreochromis_niloticus_genome ensembl oreochromis niloticus genome /path/to/bank/bowtie2db/ensembl_oreochromis_niloticus_genome
53 ensembl_ovis_aries_genome ensembl_ovis_aries_genome ensembl ovis aries genome v3 /path/to/bank/bowtie2db/ensembl_ovis_aries_genome
54 ensembl_rattus_norvegicus_genome ensembl_rattus_norvegicus_genome ensembl rattus norvegicus genome /path/to/bank/bowtie2db/ensembl_rattus_norvegicus_genome
55 ensembl_sus_scrofa_genome susScr3 ensembl sus scrofa genome /path/to/bank/bowtie2db/ensembl_sus_scrofa_genome
56 ensembl_gadus_morhua_genome ensembl_gadus_morhua_genome ensembl gadus morhua gadMor1 (Jan 2010) /path/to/bank/bowtie2db/ensembl_gadus_morhua_genome
57 ensembl_oryzias_latipes_genome ensembl_oryzias_latipes_genome ensembl oryzias latipes HdrR Oct 2005 /path/to/bank/bowtie2db/ensembl_oryzias_latipes_genome
58 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 Mycoplasma_agalactiae_GCF_000089865 /path/to/bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/bowtie2/Mycoplasma_agalactiae_GCF_000089865
59 Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_PG2_uid61619_test
60 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_uid46679_test
61 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 /path/to/bank/bowtie2db/Mycoplasma_bovis_HB0801_uid168665_test
62 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 Mycoplasma_bovis_Hubei_1_uid68691 /path/to/bank/bowtie2db/Mycoplasma_bovis_Hubei_1_uid68691_test
63 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 /path/to/bank/bowtie2db/Mycoplasma_bovis_PG45_uid60859_test
64 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 Mycoplasma_capricolum_ATCC_27343_uid58525 /path/to/bank/bowtie2db/Mycoplasma_capricolum_ATCC_27343_uid58525_test
65 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 Mycoplasma_hominis_ATCC_23114_uid41875 /path/to/bank/bowtie2db/Mycoplasma_hominis_ATCC_23114_uid41875_test
66 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 Mycoplasma_mycoides_capri_LC_95010_uid66189 /path/to/bank/bowtie2db/Mycoplasma_mycoides_capri_LC_95010_uid66189_test
67 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 Mycoplasma_mycoides_SC_Gladysdale_uid197153 /path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_Gladysdale_uid197153_test
68 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 Mycoplasma_mycoides_SC_PG1_uid58031 /path/to/bank/bowtie2db/Mycoplasma_mycoides_SC_PG1_uid58031_test
69 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_309_uid85495_test
70 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_FH_uid162027_test
71 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 Mycoplasma_pneumoniae_M129_B7_uid185759 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_B7_uid185759_test
72 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_uid57709_test
73 oryCun2_ucsc oryCun2_ucsc oryCun2 ucsc /path/to/bank/bowtie2db/oryCun2_ucsc
74 #Note that for backwards compatibility with workflows, the unique ID of
75 #an entry must be the path that was in the original loc file, because that
76 #is the value stored in the workflow for that parameter. That is why the
77 #hg19 entry above looks odd. New genomes can be better-looking.
78 #