Mercurial > repos > petrn > repeatexplorer

comparison repex_full_clustering.xml @ 13:09c1934e0c45 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petrn
date Thu, 02 Jan 2020 14:13:10 +0000
parents 3bc73f5dc785
children 7ba7048d9579
comparison
equal deleted inserted replaced
12:b4195377038d 13:09c1934e0c45
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="3.7">python</requirement> 11 <requirement type="package" version="3.7">python</requirement>
12 <requirement type="package" version="0.9.1" >pyrserve</requirement> 12 <requirement type="package" version="0.9.1" >pyrserve</requirement>
13 <requirement type="package">last</requirement> 13 <requirement type="package" version="1021" >last</requirement>
14 <requirement type="package">mafft</requirement> 14 <requirement type="package">mafft</requirement>
15 <requirement type="package">imagemagick</requirement> 15 <requirement type="package">imagemagick</requirement>
16 <requirement type="package">blast</requirement> 16 <requirement type="package">blast</requirement>
17 <requirement type="package">diamond</requirement> 17 <requirement type="package">diamond</requirement>
18 <requirement type="package">blast-legacy</requirement> 18 <requirement type="package">blast-legacy</requirement>
30 <requirement type="package">r-optparse</requirement> 30 <requirement type="package">r-optparse</requirement>
31 <requirement type="package">r-dbi</requirement> 31 <requirement type="package">r-dbi</requirement>
32 <requirement type="package">r-rsqlite</requirement> 32 <requirement type="package">r-rsqlite</requirement>
33 <requirement type="package">r-rserve</requirement> 33 <requirement type="package">r-rserve</requirement>
34 <requirement type="package">bioconductor-biostrings</requirement> 34 <requirement type="package">bioconductor-biostrings</requirement>
35 <requirement type="set_environment">REPEX</requirement>
35 </requirements> 36 </requirements>
36 <command > 37 <command >
37 make -C ${__tool_directory__};
38 export PYTHONHASHSEED=0; 38 export PYTHONHASHSEED=0;
39 ${__tool_directory__}/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
40 40
41 #if $advanced_options.advanced: 41 #if $advanced_options.advanced:
42 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx 42 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
43 --assembly_min $advanced_options.assembly_min_cluster_size 43 --assembly_min $advanced_options.assembly_min_cluster_size
44 44