Mercurial > repos > petr-novak > repeatrxplorer
comparison repex_full_clustering.xml @ 8:48704d3ce3a6 draft
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author | petr-novak |
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date | Mon, 06 Jan 2020 09:00:12 -0500 |
parents | ee6fbf1bf166 |
children | 7d88d9fabe99 |
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7:07bacdf2d9f6 | 8:48704d3ce3a6 |
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6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> | 6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" /> |
7 <exit_code range="1:" level="fatal" description="Error" /> | 7 <exit_code range="1:" level="fatal" description="Error" /> |
8 </stdio> | 8 </stdio> |
9 <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description> | 9 <description>Improved version or repeat discovery and characterization using graph based sequence clustering</description> |
10 <requirements> | 10 <requirements> |
11 <requirement type="package" version="0.9.1" >pyrserve</requirement> | |
12 <requirement type="package" version="3.7.4">python</requirement> | |
13 <requirement type="package">last</requirement> | 11 <requirement type="package">last</requirement> |
12 <requirement type="package">imagemagick</requirement> | |
14 <requirement type="package">mafft</requirement> | 13 <requirement type="package">mafft</requirement> |
15 <requirement type="package">imagemagick</requirement> | |
16 <requirement type="package">blast</requirement> | 14 <requirement type="package">blast</requirement> |
17 <requirement type="package">diamond</requirement> | 15 <requirement type="package">diamond</requirement> |
18 <requirement type="package">blast-legacy</requirement> | 16 <requirement type="package">blast-legacy</requirement> |
19 <requirement type="package">r-igraph</requirement> | 17 <requirement type="package">r-igraph</requirement> |
20 <requirement type="package">r-data.tree</requirement> | 18 <requirement type="package">r-data.tree</requirement> |
32 <requirement type="package">r-rsqlite</requirement> | 30 <requirement type="package">r-rsqlite</requirement> |
33 <requirement type="package">r-rserve</requirement> | 31 <requirement type="package">r-rserve</requirement> |
34 <requirement type="package">bioconductor-biostrings</requirement> | 32 <requirement type="package">bioconductor-biostrings</requirement> |
35 <requirement type="package" version="1.0">repex_tarean</requirement> | 33 <requirement type="package" version="1.0">repex_tarean</requirement> |
36 <requirement type="set_environment">REPEX</requirement> | 34 <requirement type="set_environment">REPEX</requirement> |
35 <requirement type="package" version="0.9.1" >pyrserve</requirement> | |
37 </requirements> | 36 </requirements> |
38 <command > | 37 <command > |
39 export PYTHONHASHSEED=0; | 38 export PYTHONHASHSEED=0; |
40 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon | 39 \${REPEX}/seqclust --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon |
41 | 40 |