# HG changeset patch
# User glogobyte
# Date 1634141689 0
# Node ID b26a6971499c78f809887bc606864ecaf9b52dfd
# Parent  023cbd52a896ae2fd89eb91fd2e6641d2c0ee3d7
Deleted selected files

diff -r 023cbd52a896 -r b26a6971499c mirbase.loc
--- a/mirbase.loc	Wed Oct 13 16:14:32 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-# bowtie2_indices.loc.sample
-# This is a *.loc.sample file distributed with Galaxy that enables tools
-# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
-# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
-# First create these data files and save them in your own data directory structure.
-# Then, create a bowtie_indices.loc file to use those indexes with tools.
-# Copy this file, save it with the same name (minus the .sample),
-# follow the format examples, and store the result in this directory.
-# The file should include an one line entry for each index set.
-# The path points to the "basename" for the set, not a specific file.
-# It has four text columns seperated by TABS.
-#
-# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
-#
-# So, for example, if you had hg18 indexes stored in:
-#
-#    /depot/data2/galaxy/hg19/bowtie2/
-#
-# containing hg19 genome and hg19.*.bt2 files, such as:
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
-#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
-#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
-#
-# then the bowtie2_indices.loc entry could look like this:
-#
-#
-hg38	Homo sapiens - GRCh38	hsa.gff3	Homo sapiens
-mm10	Mus musculus - GRCm38	mmu.gff3	Mus musculus
-BosTau5        Bos taurus - Btau_5.0.1 bta.gff3	Bos taurus
-Arabidopsis_thaliana_TAIR10	Arabidopsis thaliana - TAIR10	ath.gff3	Arabidopsis thaliana
-droSim1	Drosophila simulans - dsim_caf1	dsi.gff3	Drosophila simulans
-#
-#
-#
-#
diff -r 023cbd52a896 -r b26a6971499c mirgene.loc
--- a/mirgene.loc	Wed Oct 13 16:14:32 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-# bowtie2_indices.loc.sample
-# This is a *.loc.sample file distributed with Galaxy that enables tools
-# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
-# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
-# First create these data files and save them in your own data directory structure.
-# Then, create a bowtie_indices.loc file to use those indexes with tools.
-# Copy this file, save it with the same name (minus the .sample),
-# follow the format examples, and store the result in this directory.
-# The file should include an one line entry for each index set.
-# The path points to the "basename" for the set, not a specific file.
-# It has four text columns seperated by TABS.
-#
-# <unique_build_id>     <dbkey> <display_name>  <file_base_path>
-#
-# So, for example, if you had hg18 indexes stored in:
-#
-#    /depot/data2/galaxy/hg19/bowtie2/
-#
-# containing hg19 genome and hg19.*.bt2 files, such as:
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.fa
-#    -rw-rw-r-- 1 james   james   914M Feb 10 18:56 hg19canon.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 18:56 hg19canon.2.bt2
-#    -rw-rw-r-- 1 james   james   3.3K Feb 10 16:54 hg19canon.3.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 16:54 hg19canon.4.bt2
-#    -rw-rw-r-- 1 james   james   914M Feb 10 20:45 hg19canon.rev.1.bt2
-#    -rw-rw-r-- 1 james   james   683M Feb 10 20:45 hg19canon.rev.2.bt2
-#
-# then the bowtie2_indices.loc entry could look like this:
-#
-#
-Hsa	Human (Homo sapiens) - hg38
-Mml	Rhesus monkey (Macaca mulatta) - rheMac8
-Mmu	House mouse (Mus musculus) - mm10
-Rno	Norway rat (Rattus norvegicus) - rn6
-Cpo	Guinea pig (Cavia porcellus) - cavPor3
-Ocu	Rabbit (Oryctolagus cuniculus) - oryCun2
-Cfa	Dog (Canis familiaris) - canFam3
-Bta	Cow (Bos taurus) - bosTau8
-Dno	Nine-banded armadillo (Dasypus novemcinctus) - dasNov3
-Ete	Lesser hedgehog tenrec (Echinops telfairi) - echTel2
-Sha	Tasmanian devil (Sarcophilus harrisii) - DEVIL7_traces
-Mdo	Gray short-tailed opossum (Monodelphis domestica) - monDom5
-Oan	Platypus (Ornithorhynchus anatinus) - mOrnAna1.p.v1_plustraces
-Gga	Chicken (Gallus gallus) - galGal5
-Cli	Rock pigeon (Columba livia) - colLiv2
-Tgu	Zebra finch (Taeniopygia guttata) - taeGut3.2.4
-Ami	American alligator (Alligator mississippiensis) - allMis1
-Cpi	Western painted turtle (Chrysemys picta bellii) - chrPic1
-Aca	Green anole lizard (Anolis carolinensis) - anoCar2
-Xtr	Tropical clawed frog (Xenopus tropicalis) - xenTro7
-Dre	Zebrafish (Danio rerio) - danRer11
-Sto	Cloudy Catshark (Scyliorhinus torazame) - miRNA_loci_genome
-Cin	Sea Squirt (Ciona intestinalis) - ci3
-Bfl	Florida lancelet (Branchiostoma floridae) - BFL_v2.0
-Sko	Saccoglossus (Saccoglossus kowalevskii) - Skow_1.1
-Pfl	Ptychodera (Ptychodera flava) - Pfl
-Spu	Purple sea urchin (Strongylocentrotus purpuratus) - Spur_3.1
-Pmi	Bat starfish (Patiria miniata) - Pmin1
-Dme	Fruit fly (Drosophila melanogaster) - dm6
-Dan	Fruit fly (Drosophila ananassae) - Dana_caf1
-Dmo	Fruit fly (Drosophila mojavensis) - Dmoj_caf1
-Aae	Yellow fever mosquito (Aedes aegypti) - Aaeg_L3
-Hme	Longwing butterfly (Heliconius melpomene) - Hmel_1
-Tca	Red flour beetle (Tribolium castaneum) - Tcas5.2
-Bge	Cockroach (Blattella germanica) - Bger_2.0
-Dpu	Common water flea (Daphnia pulex) - Daphnia_pulex.V1.0
-Isc	Deer tick (Ixodes scapularis) - IscaWI
-Cel	Roundworm (Caenorhabditis elegans) - ce11
-Cbr	Roundworm (Caenorhabditis briggsae) - CB4
-Asu	Large roundworm (Ascaris suum) - ASU_PRJNA80881_plustraces
-Cte	Polychaete worm (Capitella teleta) - Capitella_teleta_v1.0
-Efe	Common brandling worm (Eisenia fetida) - Efe_combined
-Lgi	Owl limpet (Lottia gigantea) - Lotgi1
-Cgi	Pacific oyster (Crassostrea gigas) - CGI_GCA_000297895.1
-Lan	Lingula (Lingula anatina) - LinAna_1.0
-#
-#
-#
-#
-#
diff -r 023cbd52a896 -r b26a6971499c tool_data_table_conf.xml
--- a/tool_data_table_conf.xml	Wed Oct 13 16:14:32 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-<!-- Paths are relative to the value of `tool_data_path` in galaxy.ini -->
-<tables>
-    <table name="mirbase" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="tool-data/mirbase.loc" />
-    </table>
-    <table name="mirgene" comment_char="#">
-        <columns>value, name</columns>
-        <file path="tool-data/mirgene.loc" />
-    </table>
-</tables>