Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
changeset 9:9004217cddf4 draft default tip
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 23 Jul 2019 12:18:12 -0400 |
| parents | cbe62bd6e149 |
| children | |
| files | data_manager_conf.xml tool-data/all_fasta.loc.sample |
| diffstat | 2 files changed, 2 insertions(+), 20 deletions(-) [+] |
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--- a/data_manager_conf.xml Tue Jul 23 11:12:15 2019 -0400 +++ b/data_manager_conf.xml Tue Jul 23 12:18:12 2019 -0400 @@ -9,9 +9,9 @@ <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}/${version}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${version}</value_translation> <value_translation type="function">abspath</value_translation> </column> <column name="version" />
--- a/tool-data/all_fasta.loc.sample Tue Jul 23 11:12:15 2019 -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. -#