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STAR_indexes.loc.sample |
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| diff -r f7dbe77bbed5 -r c4fc8ff6e280 STAR_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/STAR_indexes.loc.sample Tue Dec 12 10:16:23 2017 -0500 |
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| b'@@ -0,0 +1,96 @@\n+#This is a sample file distributed with Galaxy that enables tools\n+#to use a directory of Bowtie indexed sequences data files. You will\n+#need to create these data files and then create a bowtie_indices.loc\n+#file similar to this one (store it in this directory) that points to\n+#the directories in which those files are stored. The bowtie_indices.loc\n+#file has this format (longer white space characters are TAB characters):\n+#\n+#<unique_build_id> <dbkey> <display_name> <file_base_path>\n+#\n+#So, for example, if you had hg18 indexed stored in \n+#/depot/data2/galaxy/bowtie/hg18/, \n+#then the bowtie_indices.loc entry would look like this:\n+#\n+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18\n+#\n+#and your /depot/data2/galaxy/bowtie/hg18/ directory\n+#would contain hg18.*.ebwt files:\n+#\n+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt\n+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt\n+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt\n+#...etc...\n+#\n+#Your bowtie_indices.loc file should include an entry per line for each\n+#index set you have stored. The "file" in the path does not actually\n+#exist, but it is the prefix for the actual index files. For example:\n+#\n+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon\n+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full\n+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19\n+#...etc...\n+#\n+\n+#Banques temporaires mises en place au debut de l installation de Galaxy\n+#AthalianaAllChr\tAthalianaAllChr\tAthalianaAllChr\t/bank/bowtiedb/AthalianaAllChr\n+#Drosophila_melanogaster_AllChr\tDrosophila_melanogaster_AllChr\tDrosophila melanogaster All Chr\t/bank/bowtiedb/Drosophila_melanogaster_AllChr\n+#Homo_sapiens_AllChr\tHomo_sapiens_AllChr\tHomo_sapiens_AllChr\t/bank/bowtiedb/Homo_sapiens_AllChr\n+#yeast.nt\tyeast.nt\tyeast nt\t/bank/bowtiedb/yeast.nt\n+\n+#Banques definitives transmises par l administrateur system sur /bank/bowtiedb\n+STAR-Arabidopsis_thaliana\tSTAR-Arabidopsis_thaliana\tSTAR-Arabidopsis_thaliana\t/bank/STARdb/STAR-Arabidopsis_thaliana\n+STAR-ensembl_gallus_gallus_genome_masked\tSTAR-ensembl_gallus_gallus_genome_masked\tSTAR-ensembl_gallus_gallus_genome_masked\t/bank/STARdb/STAR-ensembl_gallus_gallus_genome_soft_masked\n+STAR-Gorilla_gorilla\tSTAR-Gorilla_gorilla\tSTAR-Gorilla_gorilla\t/bank/STARdb/STAR-Gorilla_gorilla\n+STAR-hg38\thg38\tSTAR-ensembl_homo_sapiens_genome (GRCh38/hg38)\t/galaxydata/galaxy_bank/homo_sapiens/hg38/ensembl-89\n+STAR-Homo_sapiens_AllChr\tSTAR-Homo_sapiens_AllChr\tSTAR-Homo_sapiens_AllChr\t/bank/STARdb/STAR-Homo_sapiens_AllChr\n+STAR-ensembl_bos_taurus_genome\tSTAR-ensembl_bos_taurus_genome\tSTAR-ensembl_bos_taurus_genome\t/bank/STARdb/STAR-ensembl_bos_taurus_genome\n+STAR-ensembl_homo_sapiens_genome_masked\tSTAR-ensembl_homo_sapiens_genome_masked\tSTAR-ensembl_homo_sapiens_genome_masked\t/bank/STARdb/STAR-ensembl_homo_sapiens_genome_soft_masked\n+STAR-Macaca_mulatta\tSTAR-Macaca_mulatta\tSTAR-Macaca_mulatta\t/bank/STARdb/STAR-Macaca_mulatta\n+STAR-ensembl_bos_taurus_genome_masked\tSTAR-ensembl_bos_taurus_genome_masked\tSTAR-ensembl_bos_taurus_genome_masked\t/bank/STARdb/STAR-ensembl_bos_taurus_genome_soft_masked\n+STAR-ensembl_rattus_norvegicus_genome\tSTAR-ensembl_rattus_norvegicus_genome\tSTAR-ensembl_rattus_norvegicus_genome\t/bank/STARdb/STAR-ensembl_rattus_norvegicus_genome\n+STAR-Nomascus_leucogenys\tSTAR-Nomascus_leucogenys\tSTAR-Nomascus_leucogenys\t/bank/STARdb/STAR-Nomascus_leucogenys\n+STAR-ensembl_equus_caballus_genome\tSTAR-ensembl_equus_caballus_genome\tSTAR-ensembl_equus_caballus_genome\t/bank/STARdb/STAR-ensembl_equus_caballus_genome\n+STAR-ensembl_rattus_norvegicus_genome_masked\tSTAR-ensembl_rattus_norvegicus_genome_masked\tSTAR-ensembl_rattus_norvegicus_genome_masked\t/bank/STARdb/STAR-ensembl_rattus_norvegicus_genome_soft_masked\n+STAR-Pan_troglodytes\tSTAR-Pan_troglodytes\tSTAR-Pan_troglodytes\t/bank/STARdb/STAR-Pan_tr'..b'es_genome\tSTAR-ensembl_ovis_aries_genome\tSTAR-ensembl_ovis_aries_genome\t/bank/STARdb/STAR-ensembl_ovis_aries_genome\n+STAR-Mycoplasma_agalactiae_PG2_uid61619\tSTAR-Mycoplasma_agalactiae_PG2_uid61619\tSTAR-Mycoplasma_agalactiae_PG2_uid61619\t/bank/STARdb/STAR-Mycoplasma_agalactiae_PG2_uid61619_test\n+Mycoplasma_agalactiae_uid46679\tMycoplasma_agalactiae_uid46679\tMycoplasma_agalactiae_uid46679\t/bank/STARdb/STAR-Mycoplasma_agalactiae_uid46679_test\n+Mycoplasma_bovis_HB0801_uid168665\tMycoplasma_bovis_HB0801_uid168665\tMycoplasma_bovis_HB0801_uid168665\t/bank/STARdb/STAR-Mycoplasma_bovis_HB0801_uid168665_test\n+Mycoplasma_bovis_Hubei_1_uid68691\tMycoplasma_bovis_Hubei_1_uid68691\tMycoplasma_bovis_Hubei_1_uid68691\t/bank/STARdb/STAR-Mycoplasma_bovis_Hubei_1_uid68691_test\n+Mycoplasma_bovis_PG45_uid60859\tMycoplasma_bovis_PG45_uid60859\tMycoplasma_bovis_PG45_uid60859\t/bank/STARdb/STAR-Mycoplasma_bovis_PG45_uid60859_test\n+Mycoplasma_capricolum_ATCC_27343_uid58525\tMycoplasma_capricolum_ATCC_27343_uid58525\tMycoplasma_capricolum_ATCC_27343_uid58525\t/bank/STARdb/STAR-Mycoplasma_capricolum_ATCC_27343_uid58525_test\n+Mycoplasma_hominis_ATCC_23114_uid41875\tMycoplasma_hominis_ATCC_23114_uid41875\tMycoplasma_hominis_ATCC_23114_uid41875\t/bank/STARdb/STAR-Mycoplasma_hominis_ATCC_23114_uid41875_test\n+Mycoplasma_mycoides_capri_LC_95010_uid66189\tMycoplasma_mycoides_capri_LC_95010_uid66189\tMycoplasma_mycoides_capri_LC_95010_uid66189\t/bank/STARdb/STAR-Mycoplasma_mycoides_capri_LC_95010_uid66189_test\n+Mycoplasma_mycoides_SC_Gladysdale_uid197153\tMycoplasma_mycoides_SC_Gladysdale_uid197153\tMycoplasma_mycoides_SC_Gladysdale_uid197153\t/bank/STARdb/STAR-Mycoplasma_mycoides_SC_Gladysdale_uid197153_test\n+Mycoplasma_mycoides_SC_PG1_uid58031\tMycoplasma_mycoides_SC_PG1_uid58031\tMycoplasma_mycoides_SC_PG1_uid58031\t/bank/STARdb/STAR-Mycoplasma_mycoides_SC_PG1_uid58031_test\n+Mycoplasma_pneumoniae_309_uid85495\tMycoplasma_pneumoniae_309_uid85495\tMycoplasma_pneumoniae_309_uid85495\t/bank/STARdb/STAR-Mycoplasma_pneumoniae_309_uid85495_test\n+Mycoplasma_pneumoniae_FH_uid162027\tMycoplasma_pneumoniae_FH_uid162027\tMycoplasma_pneumoniae_FH_uid162027\t/bank/STARdb/STAR-Mycoplasma_pneumoniae_FH_uid162027_test\n+Mycoplasma_pneumoniae_M129_B7_uid185759\tMycoplasma_pneumoniae_M129_B7_uid185759\tMycoplasma_pneumoniae_M129_B7_uid185759\t/bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_B7_uid185759_test\n+Mycoplasma_pneumoniae_M129_uid57709\tMycoplasma_pneumoniae_M129_uid57709\tMycoplasma_pneumoniae_M129_uid57709\t/bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_uid57709_test\n+Mycoplasma_agalactiae_GCF_000089865\tMycoplasma_agalactiae_GCF_000089865\tMycoplasma_agalactiae_GCF_000089865\t/bank/STARdb/STAR-Mycoplasma_agalactiae_GCF_000089865\n+Assembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865\tAssembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865\tAssembly_Bacteria_2014-06-24-Mycoplasma_agalactiae_GCF_000089865\t/bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/STAR/STAR-Mycoplasma_agalactiae_GCF_000089865\n+STAR-ensembl_canis_familiaris_genome_soft_masked\tSTAR-ensembl_canis_familiaris_genome_soft_masked\tSTAR-ensembl_canis_familiaris_genome_soft_masked\t/bank/STARdb/STAR-ensembl_canis_familiaris_genome_soft_masked\n+STAR-ensembl_canis_familiaris_genome\tSTAR-ensembl_canis_familiaris_genome\tSTAR-ensembl_canis_familiaris_genome\t/bank/STARdb/STAR-ensembl_canis_familiaris_genome\n+STAR-ensembl_mus_musculus_primary_genome\tSTAR-ensembl_mus_musculus_primary_genome\tSTAR-ensembl_mus_musculus_primary_genome\t/bank/STARdb/STAR-ensembl_mus_musculus_primary_genome\n+STAR-Ovis_aries_2015-12-19_NCBI\tSTAR-Ovis_aries_2015-12-19_NCBI\tSTAR-Ovis_aries_2015-12-19_NCBI\t/bank/ncbi/genomes/Ovis_aries/current/STAR/STAR-Ovis_aries\n+#Note that for backwards compatibility with workflows, the unique ID of\n+#an entry must be the path that was in the original loc file, because that\n+#is the value stored in the workflow for that parameter. That is why the\n+#hg19 entry above looks odd. New genomes can be better-looking.\n+#\n' |