Mercurial > repos > jackcurragh > ribogalaxy_bowtie_genome
changeset 1:fca653f557d9 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Tue, 05 Apr 2022 12:51:03 +0000 |
| parents | 71f778b04f6e |
| children | 9e16178b8737 |
| files | bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample bowtie_genome_wrapper/tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 10 insertions(+), 38 deletions(-) [+] |
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--- a/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample Tue Mar 22 12:28:40 2022 +0000 +++ b/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample Tue Apr 05 12:51:03 2022 +0000 @@ -1,37 +1,9 @@ -#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... -# -#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. -# +homo_sapiens_hg19 hg19 Homo sapiens (hg19) /data2/indices/bowtie/genome/homo_sapiens_hg19_genome +homo_sapiens_hg38 hg38 Homo sapiens (hg38) /data2/indices/bowtie/genome/homo_sapiens_hg38_genome +mus_musculus_m28 m28 Mus musculus (m28) /data2/indices/bowtie/genome/mus_musculus_m28/mus_musculus_m28_genome +drosophila_melanogaster_dm3 dm3 Drosophila melanogaster (dm3) /data2/indices/bowtie/genome/drosophila_melanogater_dm3_genome +drosophila_melanogaster_dm6 dm6 Drosophila melanogaster (dm6) /data2/indices/bowtie/genome/drosophila_melanogater_dm6_genome +sacCer_9 sacCer9 Saccharomyces cerevisiae (v9) /data2/indices/bowtie/genome/sacCer_9/sacCer_9_genome +sarCer_3 sacCer3 Saccharomyces cerevisiae (v3) /data2/indices/bowtie/genome/sacCer_3/sacCer_3_genome +E_coli_K12_MG1655 e_coli Escherichia coli (K12 MG1655) /data2/indices/bowtie/genome/E_coli_K12_MG1655_genome +Arabidopsis araThal Arabidopsis thaliana (TAIR10) /data2/indices/bowtie/genome/Arabidopsis/Arabidopsis_genome
--- a/bowtie_genome_wrapper/tool_data_table_conf.xml.sample Tue Mar 22 12:28:40 2022 +0000 +++ b/bowtie_genome_wrapper/tool_data_table_conf.xml.sample Tue Apr 05 12:51:03 2022 +0000 @@ -3,6 +3,6 @@ <!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="/home/jack/projects/tools_for_Galaxy/ribogalaxy-toolshed/tools/bowtie_genome_wrapper/tool-data/bowtie_indices.loc.sample" /> + <file path="tool-data/bowtie_indices.loc.sample" /> </table> </tables>