diff STAR_indexes.loc.sample @ 5:c4fc8ff6e280 draft

Uploaded

--- /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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+#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	/bank/bowtiedb/AthalianaAllChr
+#Drosophila_melanogaster_AllChr	Drosophila_melanogaster_AllChr	Drosophila melanogaster All Chr	/bank/bowtiedb/Drosophila_melanogaster_AllChr
+#Homo_sapiens_AllChr	Homo_sapiens_AllChr	Homo_sapiens_AllChr	/bank/bowtiedb/Homo_sapiens_AllChr
+#yeast.nt	yeast.nt	yeast nt	/bank/bowtiedb/yeast.nt
+
+#Banques definitives transmises par l administrateur system sur /bank/bowtiedb
+STAR-Arabidopsis_thaliana	STAR-Arabidopsis_thaliana	STAR-Arabidopsis_thaliana	/bank/STARdb/STAR-Arabidopsis_thaliana
+STAR-ensembl_gallus_gallus_genome_masked	STAR-ensembl_gallus_gallus_genome_masked	STAR-ensembl_gallus_gallus_genome_masked	/bank/STARdb/STAR-ensembl_gallus_gallus_genome_soft_masked
+STAR-Gorilla_gorilla	STAR-Gorilla_gorilla	STAR-Gorilla_gorilla	/bank/STARdb/STAR-Gorilla_gorilla
+STAR-hg38	hg38	STAR-ensembl_homo_sapiens_genome (GRCh38/hg38)	/galaxydata/galaxy_bank/homo_sapiens/hg38/ensembl-89
+STAR-Homo_sapiens_AllChr	STAR-Homo_sapiens_AllChr	STAR-Homo_sapiens_AllChr	/bank/STARdb/STAR-Homo_sapiens_AllChr
+STAR-ensembl_bos_taurus_genome	STAR-ensembl_bos_taurus_genome	STAR-ensembl_bos_taurus_genome	/bank/STARdb/STAR-ensembl_bos_taurus_genome
+STAR-ensembl_homo_sapiens_genome_masked	STAR-ensembl_homo_sapiens_genome_masked	STAR-ensembl_homo_sapiens_genome_masked	/bank/STARdb/STAR-ensembl_homo_sapiens_genome_soft_masked
+STAR-Macaca_mulatta	STAR-Macaca_mulatta	STAR-Macaca_mulatta	/bank/STARdb/STAR-Macaca_mulatta
+STAR-ensembl_bos_taurus_genome_masked	STAR-ensembl_bos_taurus_genome_masked	STAR-ensembl_bos_taurus_genome_masked	/bank/STARdb/STAR-ensembl_bos_taurus_genome_soft_masked
+STAR-ensembl_rattus_norvegicus_genome	STAR-ensembl_rattus_norvegicus_genome	STAR-ensembl_rattus_norvegicus_genome	/bank/STARdb/STAR-ensembl_rattus_norvegicus_genome
+STAR-Nomascus_leucogenys	STAR-Nomascus_leucogenys	STAR-Nomascus_leucogenys	/bank/STARdb/STAR-Nomascus_leucogenys
+STAR-ensembl_equus_caballus_genome	STAR-ensembl_equus_caballus_genome	STAR-ensembl_equus_caballus_genome	/bank/STARdb/STAR-ensembl_equus_caballus_genome
+STAR-ensembl_rattus_norvegicus_genome_masked	STAR-ensembl_rattus_norvegicus_genome_masked	STAR-ensembl_rattus_norvegicus_genome_masked	/bank/STARdb/STAR-ensembl_rattus_norvegicus_genome_soft_masked
+STAR-Pan_troglodytes	STAR-Pan_troglodytes	STAR-Pan_troglodytes	/bank/STARdb/STAR-Pan_troglodytes
+STAR-ensembl_equus_caballus_genome_masked	STAR-ensembl_equus_caballus_genome_masked	STAR-ensembl_equus_caballus_genome_masked	/bank/STARdb/STAR-ensembl_equus_caballus_genome_soft_masked
+# STAR-ensembl_sus_scrofa_genome	susScr4	ensembl sus_scrofa genome	/bank/STARdb/STAR-ensembl_sus_scrofa_genome
+# STAR-ensembl_sus_scrofa_genome_masked	STAR-ensembl_sus_scrofa_genome_masked	STAR-ensembl_sus_scrofa_genome_masked	/bank/STARdb/STAR-ensembl_sus_scrofa_genome_soft_masked
+#
+STAR-ensembl_sus_scrofa_V10.2	susScr3	Ensembl sus_scrofa genome V10.2	/galaxydata/galaxy_bank/sus_scrofa/Sscrofa10.2/ensembl-89/STAR-ensembl_sus_scrofa_genome
+STAR-ensembl_sus_scrofa_V11.1	susScr11	Ensembl sus_scrofa genome V11.1	/galaxydata/galaxy_bank/sus_scrofa/Sscrofa11.1/ensembl-90/STAR-ensembl_sus_scrofa_genome
+#
+STAR-Papio_anubis	STAR-Papio_anubis	STAR-Papio_anubis	/bank/STARdb/STAR-Papio_anubis
+STAR-ensembl_gallus_gallus_genome	STAR-ensembl_gallus_gallus_genome	STAR-ensembl_gallus_gallus_genome	/bank/STARdb/STAR-ensembl_gallus_gallus_genome
+STAR-Pongo_abelii	STAR-Pongo_abelii	STAR-Pongo_abelii	/bank/STARdb/STAR-Pongo_abelii
+STAR-ensembl_danio_rerio_genome	STAR-ensembl_danio_rerio_genome	STAR-ensembl_danio_rerio_genome	/bank/STARdb/STAR-ensembl_danio_rerio_genome
+STAR-ensembl_danio_rerio_genome_masked	STAR-ensembl_danio_rerio_genome_masked	STAR-ensembl_danio_rerio_genome_masked	/bank/STARdb/STAR-ensembl_danio_rerio_genome_soft_masked
+STAR-ensembl_oreochromis_niloticus_genome	STAR-ensembl_oreochromis_niloticus_genome	STAR-ensembl_oreochromis_niloticus_genome	/bank/STARdb/STAR-ensembl_oreochromis_niloticus_genome
+STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal	STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal	STAR-ensembl_oreochromis_niloticus_genome_nonchomosomal	/bank/STARdb/STAR-ensembl_oreochromis_niloticus_genome_non_chromosomal
+STAR_oryCun2_ucsc	STAR_oryCun2_ucsc	STAR oryCun2 ucsc	/bank/STARdb/STAR-oryCun2_ucsc
+STAR-Capra_hircus	STAR-Capra_hircus	STAR-Capra_hircus	/bank/STARdb/STAR-Capra_hircus
+STAR-ensembl_ovis_aries_genome	STAR-ensembl_ovis_aries_genome	STAR-ensembl_ovis_aries_genome	/bank/STARdb/STAR-ensembl_ovis_aries_genome
+STAR-Mycoplasma_agalactiae_PG2_uid61619	STAR-Mycoplasma_agalactiae_PG2_uid61619	STAR-Mycoplasma_agalactiae_PG2_uid61619	/bank/STARdb/STAR-Mycoplasma_agalactiae_PG2_uid61619_test
+Mycoplasma_agalactiae_uid46679	Mycoplasma_agalactiae_uid46679	Mycoplasma_agalactiae_uid46679	/bank/STARdb/STAR-Mycoplasma_agalactiae_uid46679_test
+Mycoplasma_bovis_HB0801_uid168665	Mycoplasma_bovis_HB0801_uid168665	Mycoplasma_bovis_HB0801_uid168665	/bank/STARdb/STAR-Mycoplasma_bovis_HB0801_uid168665_test
+Mycoplasma_bovis_Hubei_1_uid68691	Mycoplasma_bovis_Hubei_1_uid68691	Mycoplasma_bovis_Hubei_1_uid68691	/bank/STARdb/STAR-Mycoplasma_bovis_Hubei_1_uid68691_test
+Mycoplasma_bovis_PG45_uid60859	Mycoplasma_bovis_PG45_uid60859	Mycoplasma_bovis_PG45_uid60859	/bank/STARdb/STAR-Mycoplasma_bovis_PG45_uid60859_test
+Mycoplasma_capricolum_ATCC_27343_uid58525	Mycoplasma_capricolum_ATCC_27343_uid58525	Mycoplasma_capricolum_ATCC_27343_uid58525	/bank/STARdb/STAR-Mycoplasma_capricolum_ATCC_27343_uid58525_test
+Mycoplasma_hominis_ATCC_23114_uid41875	Mycoplasma_hominis_ATCC_23114_uid41875	Mycoplasma_hominis_ATCC_23114_uid41875	/bank/STARdb/STAR-Mycoplasma_hominis_ATCC_23114_uid41875_test
+Mycoplasma_mycoides_capri_LC_95010_uid66189	Mycoplasma_mycoides_capri_LC_95010_uid66189	Mycoplasma_mycoides_capri_LC_95010_uid66189	/bank/STARdb/STAR-Mycoplasma_mycoides_capri_LC_95010_uid66189_test
+Mycoplasma_mycoides_SC_Gladysdale_uid197153	Mycoplasma_mycoides_SC_Gladysdale_uid197153	Mycoplasma_mycoides_SC_Gladysdale_uid197153	/bank/STARdb/STAR-Mycoplasma_mycoides_SC_Gladysdale_uid197153_test
+Mycoplasma_mycoides_SC_PG1_uid58031	Mycoplasma_mycoides_SC_PG1_uid58031	Mycoplasma_mycoides_SC_PG1_uid58031	/bank/STARdb/STAR-Mycoplasma_mycoides_SC_PG1_uid58031_test
+Mycoplasma_pneumoniae_309_uid85495	Mycoplasma_pneumoniae_309_uid85495	Mycoplasma_pneumoniae_309_uid85495	/bank/STARdb/STAR-Mycoplasma_pneumoniae_309_uid85495_test
+Mycoplasma_pneumoniae_FH_uid162027	Mycoplasma_pneumoniae_FH_uid162027	Mycoplasma_pneumoniae_FH_uid162027	/bank/STARdb/STAR-Mycoplasma_pneumoniae_FH_uid162027_test
+Mycoplasma_pneumoniae_M129_B7_uid185759	Mycoplasma_pneumoniae_M129_B7_uid185759	Mycoplasma_pneumoniae_M129_B7_uid185759	/bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_B7_uid185759_test
+Mycoplasma_pneumoniae_M129_uid57709	Mycoplasma_pneumoniae_M129_uid57709	Mycoplasma_pneumoniae_M129_uid57709	/bank/STARdb/STAR-Mycoplasma_pneumoniae_M129_uid57709_test
+Mycoplasma_agalactiae_GCF_000089865	Mycoplasma_agalactiae_GCF_000089865	Mycoplasma_agalactiae_GCF_000089865	/bank/STARdb/STAR-Mycoplasma_agalactiae_GCF_000089865
+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	/bank/ncbi/genomes/Assembly_Bacteria/Assembly_Bacteria_2014-06-24/STAR/STAR-Mycoplasma_agalactiae_GCF_000089865
+STAR-ensembl_canis_familiaris_genome_soft_masked	STAR-ensembl_canis_familiaris_genome_soft_masked	STAR-ensembl_canis_familiaris_genome_soft_masked	/bank/STARdb/STAR-ensembl_canis_familiaris_genome_soft_masked
+STAR-ensembl_canis_familiaris_genome	STAR-ensembl_canis_familiaris_genome	STAR-ensembl_canis_familiaris_genome	/bank/STARdb/STAR-ensembl_canis_familiaris_genome
+STAR-ensembl_mus_musculus_primary_genome	STAR-ensembl_mus_musculus_primary_genome	STAR-ensembl_mus_musculus_primary_genome	/bank/STARdb/STAR-ensembl_mus_musculus_primary_genome
+STAR-Ovis_aries_2015-12-19_NCBI	STAR-Ovis_aries_2015-12-19_NCBI	STAR-Ovis_aries_2015-12-19_NCBI	/bank/ncbi/genomes/Ovis_aries/current/STAR/STAR-Ovis_aries
+#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.
+#