SHARE
TWEET

genomeannotatorncbi

a guest Nov 16th, 2012 3 Never
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
  1. <?xml version="1.0" encoding="UTF-8"?>
  2. <!--
  3. This Diya conf file can be used to take 454 assemblies and a *qual file as input
  4. and output an annotated Genbank file and corresponding ASN.1 that can be submitted to
  5. NCBI.
  6.  
  7. Example command:
  8.  
  9. nohup /usr/lib/perl5/site_perl/5.8.8/diya.pl
  10. -conf genome-annotator-for-ncbi.xml \
  11. -set MYUNIREFD=/Jake/data/mirror/uniprot/uniref50.fasta
  12. -set MYSTRAIN=test0001 \
  13. -set MYSPECIES='Test test'
  14. -set MYRPSD=/Jake/data/mirror/ncbi/CDD/Cdd
  15. -set MYSEQID=test0001 \
  16. -set MYCLUSTERS=/Jake/data/mirror/ncbi/CDD/Clusters.bcp \
  17. -set MYCDD=/Jake/data/mirror/ncbi/CDD/cddid_all.tbl
  18. -set MYQUALFILE=454MiniContigs.qual \
  19. -set MYTAXID=12345 454MiniContigs.fna > test0001.out &
  20.  
  21. 1. copy all relevant files to a working directory
  22. 2. run glimmer3
  23. 3. run blastp of predicted peptides against UniRef50
  24. 4. run rpsblast of predicted peptides against CDD
  25. 5. run tRNAscanSE
  26. 6. run rnammer
  27. 7. run CRT
  28. 8. run phobos
  29. 9. run cmsearch
  30. 10. correct of annotation text
  31. 11. create ASN and associated files for NCBI submission
  32.  
  33. -bin /Jake/apps/bin -infile INPUTFILE -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR -newbler 200:5
  34. assemble_pseudocontig make-single-fa MARC::glimmer3 extractCDS MARC::blastpCDS MARC::rpsblastCDS MARC::tRNAscanSE MARC::rnammer MARC::CRT MARC::phobos MARC::cmsearch gbconvert cleanup
  35.  
  36. assemble_pseudocontig make-single-fa MARC::glimmer3 extractCDS MARC::blastpCDS <<<< works
  37. -->
  38.  
  39. <conf>
  40.   <order>
  41.    <names>assemble_pseudocontig make-single-fa MARC::glimmer3 extractCDS MARC::blastpCDS MARC::rpsblastCDS
  42.    </names>
  43.   </order>
  44.     <script>
  45.     <name>assemble_pseudocontig</name>
  46.     <executable>diya-assemble_pseudocontig.pl</executable>
  47.     <command>-infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR</command>
  48.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  49.     <inputfrom></inputfrom>
  50.     <inputformat></inputformat>
  51.   </script>
  52.   <script>
  53.     <name>make-single-fa</name>
  54.     <executable>make-single-fa.pl</executable>
  55.     <command>MYSEQID.gbk OUTPUTDIR</command>
  56.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  57.     <inputfrom></inputfrom>
  58.     <inputformat></inputformat>
  59.   </script>
  60.   <parser>
  61.     <name>MARC::glimmer3</name>
  62.     <executable>g3-from-scratch2.csh</executable>
  63.     <command>MYSEQID.fa MYSEQID OUTPUTDIR</command>
  64.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  65.     <inputfrom></inputfrom>
  66.     <inputformat></inputformat>
  67.   </parser>
  68.   <script>
  69.     <name>extractCDS</name>
  70.     <executable>extractCDS.pl</executable>
  71.     <command>INPUTFILE OUTPUTFILE OUTPUTDIR</command>
  72.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  73.     <inputfrom>MARC::glimmer3</inputfrom>
  74.     <inputformat></inputformat>
  75.   </script>
  76.   <parser>
  77.     <name>MARC::blastpCDS</name>
  78.     <executable>blastall</executable>
  79.     <command>-i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8</command>
  80.     <home>/usr/bin</home>
  81.     <inputformat></inputformat>
  82.     <inputfrom>extractCDS</inputfrom>
  83.   </parser>
  84.   <parser>
  85.     <name>MARC::rpsblastCDS</name>
  86.     <executable>rpsblast</executable>
  87.     <command>-d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8</command>
  88.     <home>/usr/bin</home>
  89.     <inputformat></inputformat>
  90.     <inputfrom>extractCDS</inputfrom>
  91.   </parser>
  92.   <parser>
  93.     <name>MARC::tRNAscanSE</name>
  94.     <executable>tRNAscan-SE</executable>
  95.     <command>-B -o OUTPUTFILE MYSEQID.fa</command>
  96.     <home>/home/jasperk/Apps/tRNAscan-SE-1.3.1</home>
  97.     <inputformat></inputformat>
  98.     <inputfrom></inputfrom>
  99.   </parser>
  100.   <parser>
  101.     <name>MARC::rnammer</name>
  102.     <executable>rnammer</executable>
  103.     <command>-S bac --gff OUTPUTFILE MYSEQID.fa</command>
  104.     <home>/Jake/apps/rnammer-1.2</home>
  105.     <inputformat></inputformat>
  106.     <inputfrom></inputfrom>
  107.   </parser>
  108.   <parser>
  109.     <name>MARC::CRT</name>
  110.     <executable>java</executable>
  111.     <command>-cp /Jake/apps/CRT/CRT1.2-CLI.jar crt MYSEQID.fa OUTPUTFILE</command>
  112.     <home>/usr/bin</home>
  113.     <inputformat></inputformat>
  114.     <inputfrom></inputfrom>
  115.   </parser>
  116.   <script>
  117.     <name>make-sRNAscanner-input</name>
  118.     <executable>make-sRNAscanner-input.pl</executable>
  119.     <command>MYSEQID OUTPUTDIR</command>
  120.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  121.     <inputfrom></inputfrom>
  122.     <inputformat></inputformat>
  123.   </script>
  124.   <parser>
  125.     <name>MARC::sRNAscanner</name>
  126.     <executable>sRNAscanner</executable>
  127.     <command>OUTPUTDIR/Input.data</command>
  128.     <home>/Jake/apps/sRNAscanner</home>
  129.     <inputformat></inputformat>
  130.     <inputfrom></inputfrom>
  131.   </parser>
  132.   <parser>
  133.     <name>MARC::cmsearch</name>
  134.     <executable>cmsearch</executable>
  135.     <command>--tabfile OUTPUTFILE -E 1.0e-20 -o MYSEQID.cmsearch /Jake/data/mirror/Rfam-10.0/sRNAs.cm MYSEQID.fa</command>
  136.     <home>/Jake/apps/infernal-1.0.2/bin</home>
  137.     <inputformat></inputformat>
  138.     <inputfrom></inputfrom>
  139.   </parser>
  140.   <parser>
  141.     <name>MARC::phobos</name>
  142.     <executable>phobos-linux-gcc4.1.2</executable>
  143.     <command>-M exact -u 9 -U 1000 --outputFormat 2 MYSEQID.fa OUTPUTFILE</command>
  144.     <home>/Jake/apps/bin</home>
  145.     <inputformat></inputformat>
  146.     <inputfrom></inputfrom>
  147.   </parser>
  148.   <script>
  149.     <name>gbconvert</name>
  150.     <executable>gbconvert.pl</executable>
  151.     <command>-agp -q MYQUALFILE -t MYTAXID INPUTFILE.gbk</command>
  152.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  153.     <inputformat></inputformat>
  154.     <inputfrom>MARC::cmsearch</inputfrom>
  155.   </script>
  156.   <script>
  157.     <name>cleanup</name>
  158.     <executable>cleanup.sh</executable>
  159.     <command>MYSEQID OUTPUTDIR</command>
  160.     <home>/home/jasperk/Apps/DIYA-master/scripts</home>
  161.     <inputformat></inputformat>
  162.     <inputfrom></inputfrom>
  163.   </script>
  164.   <run>
  165.     <mode>serial</mode>
  166.   </run>
  167. </conf>
RAW Paste Data
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy. OK, I Understand
 
Top