Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 3:3d12fd3b7cae draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Fri, 19 Oct 2018 10:26:13 -0400 |
| parents | f7d9182bdcab |
| children | ef2031036f47 |
| files | tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 1 insertions(+), 24 deletions(-) [+] |
line wrap: on
line diff
--- a/tool-data/all_fasta.loc.sample Fri Oct 19 09:53:44 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -#
--- a/tool_data_table_conf.xml.sample Fri Oct 19 09:53:44 2018 -0400 +++ b/tool_data_table_conf.xml.sample Fri Oct 19 10:26:13 2018 -0400 @@ -1,10 +1,5 @@ <tables> - <!-- Locations of all fasta files under genome directory --> - <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> - </table> - <!-- Locations of indexes in the kallisto mapper format --> + <!-- Locations of indexes in salmon mapper format --> <table name="salmon_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/salmon_indexes.loc" />