Mercurial > repos > greg > cfsan_snp_pipeline_map_reads
changeset 1:85e400e1f2dd draft default tip
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Nov 2023 18:36:23 +0000 |
| parents | e589aadb5a80 |
| children | |
| files | tool-data/bowtie2_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 3 files changed, 70 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Thu Nov 23 18:36:23 2023 +0000 @@ -0,0 +1,54 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> +</tables> +(base) o1-3s4vnf2:bowtie2 gvk$ cd ttol-da +-bash: cd: ttol-da: No such file or directory +(base) o1-3s4vnf2:bowtie2 gvk$ cd tool-data/ +(base) o1-3s4vnf2:tool-data gvk$ ll +total 8 +drwxr-xr-x 3 gvk staff 96 Jan 31 2018 . +drwxr-xr-x 8 gvk staff 256 Nov 23 13:26 .. +-rw-r--r-- 1 gvk staff 1713 Jan 31 2018 bowtie2_indices.loc.sample +(base) o1-3s4vnf2:tool-data gvk$ cat bowtie2_indices.loc.sample +# 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: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 +# +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Nov 23 18:36:23 2023 +0000 @@ -0,0 +1,8 @@ +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> +</tables> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Nov 23 18:36:23 2023 +0000 @@ -0,0 +1,8 @@ +<tables> + <!-- Locations of all fasta files under tool-data/genome directory --> + <table name="bowtie2_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/bowtie2_indexes.loc" /> + </table> +</tables> +