Mercurial > repos > sarahinraauzeville > rnaseq_tophat2
changeset 0:15aa80493a82 draft
Uploaded
| author | sarahinraauzeville |
|---|---|
| date | Thu, 11 Feb 2016 08:45:06 -0500 |
| parents | |
| children | 038c61725cfb |
| files | tophat_indexes.loc |
| diffstat | 1 files changed, 78 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tophat_indexes.loc Thu Feb 11 08:45:06 2016 -0500 @@ -0,0 +1,78 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# + +#Banques temporaires mises en place au debut de l installation de Galaxy +#AthalianaAllChr AthalianaAllChr AthalianaAllChr /path/to/bank/bowtiedb/AthalianaAllChr +#Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster All Chr /path/to/bank/bowtiedb/Drosophila_melanogaster_AllChr +#Homo_sapiens_AllChr Homo_sapiens_AllChr Homo_sapiens_AllChr /path/to/bank/bowtiedb/Homo_sapiens_AllChr +#yeast.nt yeast.nt yeast nt /path/to/bank/bowtiedb/yeast.nt + +#Banques definitives transmises par l administrateur system sur /path/to/bank/bowtiedb +Arabidopsis_thaliana Arabidopsis_thaliana Arabidopsis thaliana /path/to/bank/bowtie2db/Arabidopsis_thaliana +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 +Capra_hircus Capra_hircus Capra_hircus /path/to/bank/bowtie2db/Capra_hircus +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 +Drosophila_melanogaster_AllChr Drosophila_melanogaster_AllChr Drosophila melanogaster AllChr /path/to/bank/bowtie2db/Drosophila_melanogaster_AllChr +ensembl_bos_taurus_genome ensembl_bos_taurus_genome ensembl bos taurus genome /path/to/bank/bowtie2db/ensembl_bos_taurus_genome +ensembl_danio_rerio_genome ensembl_danio_rerio_genome ensembl danio rerio genome /path/to/bank/bowtie2db/ensembl_danio_rerio_genome +ensembl_equus_caballus_genome ensembl_equus_caballus_genome ensembl equus caballus genome /path/to/bank/bowtie2db/ensembl_equus_caballus_genome +ensembl_gallus_gallus_genome ensembl_gallus_gallus_genome ensembl gallus gallus genome /path/to/bank/bowtie2db/ensembl_gallus_gallus_genome +ensembl_homo_sapiens_genome ensembl_homo_sapiens_genome ensembl homo sapiens genome /path/to/bank/bowtie2db/ensembl_homo_sapiens_genome +ensembl_mus_musculus_genome ensembl_mus_musculus_genome ensembl mus musculus genome /path/to/bank/bowtie2db/ensembl_mus_musculus_genome +ensembl_oreochromis_niloticus_genome ensembl_oreochromis_niloticus_genome ensembl oreochromis niloticus genome /path/to/bank/bowtie2db/ensembl_oreochromis_niloticus_genome +ensembl_ovis_aries_genome ensembl_ovis_aries_genome ensembl ovis aries genome v3 /path/to/bank/bowtie2db/ensembl_ovis_aries_genome +ensembl_rattus_norvegicus_genome ensembl_rattus_norvegicus_genome ensembl rattus norvegicus genome /path/to/bank/bowtie2db/ensembl_rattus_norvegicus_genome +ensembl_sus_scrofa_genome susScr3 ensembl sus scrofa genome /path/to/bank/bowtie2db/ensembl_sus_scrofa_genome +ensembl_gadus_morhua_genome ensembl_gadus_morhua_genome ensembl gadus morhua gadMor1 (Jan 2010) /path/to/bank/bowtie2db/ensembl_gadus_morhua_genome +ensembl_oryzias_latipes_genome ensembl_oryzias_latipes_genome ensembl oryzias latipes HdrR Oct 2005 /path/to/bank/bowtie2db/ensembl_oryzias_latipes_genome +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 +Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 Mycoplasma_agalactiae_PG2_uid61619 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_PG2_uid61619_test +Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 Mycoplasma_agalactiae_uid46679 /path/to/bank/bowtie2db/Mycoplasma_agalactiae_uid46679_test +Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 Mycoplasma_bovis_HB0801_uid168665 /path/to/bank/bowtie2db/Mycoplasma_bovis_HB0801_uid168665_test +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 +Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 Mycoplasma_bovis_PG45_uid60859 /path/to/bank/bowtie2db/Mycoplasma_bovis_PG45_uid60859_test +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 +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 +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 +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 +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 +Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 Mycoplasma_pneumoniae_309_uid85495 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_309_uid85495_test +Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 Mycoplasma_pneumoniae_FH_uid162027 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_FH_uid162027_test +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 +Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 Mycoplasma_pneumoniae_M129_uid57709 /path/to/bank/bowtie2db/Mycoplasma_pneumoniae_M129_uid57709_test +oryCun2_ucsc oryCun2_ucsc oryCun2 ucsc /path/to/bank/bowtie2db/oryCun2_ucsc +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +#