Mercurial > repos > petr-novak > repeatexplorer2_testing
comparison repex_full_clustering.xml @ 4:72c028e3e70e draft
Uploaded
author | petr-novak |
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date | Thu, 08 Apr 2021 10:31:53 +0000 |
parents | d1f67a13b70f |
children | 397394c00bf7 |
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3:d1f67a13b70f | 4:72c028e3e70e |
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1 <tool id="repeatexplorer2_dev" name="RepeatExplorer2 clustering: " version="2.3.8" > | 1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" > |
2 <stdio> | 2 <stdio> |
3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> | 3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" /> |
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> | 4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> |
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> | 5 <regex match="error" source="stderr" level="fatal" description="Unknown error" /> |
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="1.18.1">numpy</requirement> | 11 <container type="singularity">shub://repeatexplorer/repex_tarean:0.3.8.dbaa07f</container> |
12 <requirement type="package" version="0.8">logomaker</requirement> | |
13 <requirement type="package" version="1.0.3">pandas</requirement> | |
14 <requirement type="package" version="3.1.3">matplotlib</requirement> | |
15 <requirement type="package">last</requirement> | |
16 <requirement type="package">imagemagick</requirement> | |
17 <requirement type="package">mafft</requirement> | |
18 <requirement type="package">blast</requirement> | |
19 <requirement type="package" version="0.9.29" >diamond</requirement> | |
20 <requirement type="package">blast-legacy</requirement> | |
21 <requirement type="package">r-igraph</requirement> | |
22 <requirement type="package">r-data.tree</requirement> | |
23 <requirement type="package">r-stringr</requirement> | |
24 <requirement type="package">r-r2html</requirement> | |
25 <requirement type="package">r-hwriter</requirement> | |
26 <requirement type="package">r-dt</requirement> | |
27 <requirement type="package">r-scales</requirement> | |
28 <requirement type="package">r-plotrix</requirement> | |
29 <requirement type="package">r-png</requirement> | |
30 <requirement type="package">r-plyr</requirement> | |
31 <requirement type="package">r-dplyr</requirement> | |
32 <requirement type="package">r-optparse</requirement> | |
33 <requirement type="package">r-dbi</requirement> | |
34 <requirement type="package">r-rsqlite</requirement> | |
35 <requirement type="package">r-rserve</requirement> | |
36 <requirement type="package">bioconductor-biostrings</requirement> | |
37 <requirement type="package" version="2.3.8">repex_tarean_dev</requirement> | |
38 <requirement type="set_environment">REPEX</requirement> | |
39 <requirement type="set_environment">REPEX_VERSION</requirement> | |
40 <requirement type="package" version="0.9.1" >pyrserve</requirement> | |
41 </requirements> | 12 </requirements> |
42 <command > | 13 <command> |
43 export PYTHONHASHSEED=0; | 14 export PYTHONHASHSEED=0; |
44 \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon | 15 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon |
45 | 16 |
46 #if $advanced_options.advanced: | 17 #if $advanced_options.advanced: |
47 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx | 18 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx |
48 --assembly_min $advanced_options.assembly_min_cluster_size | 19 --assembly_min $advanced_options.assembly_min_cluster_size |
49 | 20 |
62 ${FastaFile} >stdout.log 2> stderr.log ; | 33 ${FastaFile} >stdout.log 2> stderr.log ; |
63 echo "STDOUT CONTENT:" >> ${log} ; | 34 echo "STDOUT CONTENT:" >> ${log} ; |
64 cat stdout.log >> ${log} ; | 35 cat stdout.log >> ${log} ; |
65 echo "STDERR CONTENT:" >> ${log}; | 36 echo "STDERR CONTENT:" >> ${log}; |
66 cat stderr.log >> ${log} && | 37 cat stderr.log >> ${log} && |
67 \${REPEX}/stderr_filter.py stderr.log && | 38 /opt/repex_tarean/stderr_filter.py stderr.log && |
68 cd tarean_output && | 39 cd tarean_output && |
69 zip -r ${ReportArchive}.zip * && | 40 zip -r ${ReportArchive}.zip * && |
70 mv ${ReportArchive}.zip ${ReportArchive} && | 41 mv ${ReportArchive}.zip ${ReportArchive} && |
71 cp index.html ${ReportFile} && | 42 cp index.html ${ReportFile} && |
72 mkdir ${ReportFile.files_path} && | 43 mkdir ${ReportFile.files_path} && |