| Previous changeset 13:09c1934e0c45 (2020-01-02) Next changeset 15:993c01ddfdd4 (2020-01-02) |
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Commit message:
Uploaded |
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modified:
repex_tarean.xml |
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| diff -r 09c1934e0c45 -r ac3abb440e3f repex_tarean.xml --- a/repex_tarean.xml Thu Jan 02 14:13:10 2020 +0000 +++ b/repex_tarean.xml Thu Jan 02 14:13:27 2020 +0000 |
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| @@ -7,11 +7,9 @@ </stdio> <description>Identification of genomic tandem repeats from NGS data</description> <requirements> - <requirement type="package" version="1.0">repex_tarean</requirement> - <requirement type="set_environment">REPEX</requirement> <requirement type="package" version="3.7">python</requirement> <requirement type="package" version="0.9.1" >pyrserve</requirement> - <requirement type="package" >last</requirement> + <requirement type="package" version="1021" >last</requirement> <requirement type="package">mafft</requirement> <requirement type="package">imagemagick</requirement> <requirement type="package">blast</requirement> @@ -33,12 +31,11 @@ <requirement type="package">r-rsqlite</requirement> <requirement type="package">r-rserve</requirement> <requirement type="package">bioconductor-biostrings</requirement> + <requirement type="set_environment">REPEX</requirement> </requirements> - <command detect_errors="exit_code"> - make -C ${__tool_directory__}; export PYTHONHASHSEED=0; - ${__tool_directory__}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode + \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging #if $advanced_options.custom_library.options_custom_library : |