Mercurial > repos > petr-novak > repeatrxplorer

comparison repex_full_clustering.xml @ 8:48704d3ce3a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petr-novak
date Mon, 06 Jan 2020 09:00:12 -0500
parents ee6fbf1bf166
children 7d88d9fabe99
comparison
equal deleted inserted replaced
7:07bacdf2d9f6 8:48704d3ce3a6
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